diff --git a/Plumed.cmake b/Plumed.cmake
new file mode 100644
index 0000000..f66e115
--- /dev/null
+++ b/Plumed.cmake
@@ -0,0 +1,3 @@
+# PLUMED: shared installation
+set(PLUMED_LOAD  /home/jas02/software/PLUMED/2.1.3-foss-2015b/lib/plumed///src/lib/libplumed.so -ldl )
+set(PLUMED_DEPENDENCIES  /home/jas02/software/PLUMED/2.1.3-foss-2015b/lib/plumed///src/lib/libplumed.so)
diff --git a/Plumed.h b/Plumed.h
new file mode 100644
index 0000000..16da74a
--- /dev/null
+++ b/Plumed.h
@@ -0,0 +1,494 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2014 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_wrapper_Plumed_h
+#define __PLUMED_wrapper_Plumed_h
+
+/**
+\page ReferencePlumedH Reference for interfacing MD codes with PLUMED
+
+  Plumed.h and Plumed.c contain the external plumed interface, which is used to
+  integrate it with MD engines. This interface is very general, and is expected
+  not to change across plumed versions. Plumed.c also implements a dummy version
+  of the interface, so as to allow a code to be fully linked even if the plumed
+  library is not available yet. These files could be directly included in the official
+  host MD distribution. In this manner, it will be sufficient to link the plumed
+  library at link time (on all systems) or directly at runtime (on system where
+  dynamic loading is enabled) to include plumed features.
+
+  Why is Plumed.c written in C and not C++? The reason is that the resulting Plumed.o
+  needs to be linked with the host MD code immediately (whereas the rest of plumed
+  could be linked a posteriori). Imagine the MD code is written in FORTRAN: when we
+  link the Plumed.o file we would like not to need any C++ library linked. In this
+  manner, we do not need to know which C++ compiler will be used to compile plumed.
+  The C++ library is only linked to the "rest" of plumed, which actually use it.
+  Anyway, Plumed.c is written in such a manner to allow its compilation also in C++
+  (C++ is a bit stricter than C; compatibility is checked when PlumedStatic.cpp,
+  which basically includes Plumed.c, is compiled with the C++ compiler). This will
+  allow e.g. MD codes written in C++ to just incorporate Plumed.c (maybe renamed into
+  Plumed.cpp), without the need of configuring a plain C compiler.
+
+  Plumed interface can be used from C, C++ and FORTRAN. Everything concerning plumed
+  is hidden inside a single object type, which is described in C by a structure
+  (struct \ref plumed), in C++ by a class (PLMD::Plumed) and in FORTRAN by a
+  fixed-length string (CHARACTER(LEN=32)). Obviously C++ can use both struct
+  and class interfaces, but the first should be preferred. The reference interface
+  is the C one, whereas FORTRAN and C++ interfaces are implemented as wrappers
+  around it.
+
+  In the C++ interface, all the routines are implemented as methods of PLMD::Plumed.
+  In the C and FORTRAN interfaces, all the routines are named plumed_*, to
+  avoid potential name clashes. Notice that the entire plumed library
+  is implemented in C++, and it is hidden inside the PLMD namespace.
+
+  Handlers to the plumed object can be converted among different representations,
+  to allow inter-operability among languages. In C, there are tools to convert
+  to/from FORTRAN, whereas in C++ there are tools to convert to/from FORTRAN and C.
+
+  These handlers only contain a pointer to the real structure, so that
+  when a plumed object is brought from one language to another,
+  it brings a reference to the same environment.
+
+  Moreover, to simplify life in all cases where a single Plumed object is
+  required for the entire simulation (which covers most of the practical
+  applications with conventional MD codes) it is possible to take advantage
+  of a global interface, which is implicitly referring to a unique global instance.
+  The global object should still be initialized and finalized properly.
+
+  The basic method to send a message to plumed is
+\verbatim
+  (C) plumed_cmd
+  (C++) PLMD::Plumed::cmd
+  (FORTRAN)  PLUMED_F_CMD
+\endverbatim
+
+  To initialize a plumed object, use:
+\verbatim
+  (C)        plumed_create
+  (C++)      (constructor of PLMD::Plumed)
+  (FORTRAN)  PLUMED_F_CREATE
+\endverbatim
+
+  To finalize it, use
+\verbatim
+  (C)        plumed_finalize
+  (C++)      (destructor of PLMD::Plumed)
+  (FORTRAN)  PLUMED_F_FINALIZE
+\endverbatim
+
+  To access to the global-object, use
+\verbatim
+  (C)        plumed_gcreate, plumed_gfinalize, plumed_gcmd
+  (C++)      PLMD::Plumed::gcreate, PLMD::Plumed::gfinalize, PLMD::Plumed::gcmd
+  (FORTRAN)  PLUMED_F_GCREATE, PLUMED_F_GFINALIZE, PLUMED_F_GCMD
+\endverbatim
+
+  To check if the global object has been initialized, use
+\verbatim
+  (C)        plumed_ginitialized
+  (C++)      PLMD::Plumed::ginitialized
+  (FORTRAN)  PLUMED_F_GINITIALIZED
+\endverbatim
+
+  To check if plumed library is available (this is useful for runtime linking), use
+\verbatim
+  (C)        plumed_installed 
+  (C++)      PLMD::Plumed::installed
+  (FORTRAN)  PLUMED_F_INSTALLED
+\endverbatim
+
+  To convert handlers use
+\verbatim
+  (C)        plumed_c2f                 (C to FORTRAN)
+  (C)        plumed_f2c                 (FORTRAN to C)
+  (C++)      Plumed(plumed) constructor (C to C++)
+  (C++)      operator plumed() cast     (C++ to C)
+  (C++)      Plumed(char*)  constructor (FORTRAN to C++)
+  (C++)      toFortran(char*)           (C++ to FORTRAN)
+\endverbatim
+
+\verbatim
+  FORTRAN interface
+    SUBROUTINE PLUMED_F_INSTALLED(i)
+      INTEGER,           INTENT(OUT)   :: i
+    SUBROUTINE PLUMED_F_GINITIALIZED(i)
+      INTEGER,           INTENT(OUT)   :: i
+    SUBROUTINE PLUMED_F_GCREATE()
+    SUBROUTINE PLUMED_F_GCMD(key,val)
+      CHARACTER(LEN=*), INTENT(IN)     :: key
+      UNSPECIFIED_TYPE, INTENT(INOUT)  :: val(*)
+    SUBROUTINE PLUMED_F_GFINALIZE()
+    SUBROUTINE PLUMED_F_GLOBAL(p)
+      CHARACTER(LEN=32), INTENT(OUT)   :: p
+    SUBROUTINE PLUMED_F_CREATE(p)
+      CHARACTER(LEN=32), INTENT(OUT)   :: p
+    SUBROUTINE PLUMED_F_CMD(p,key,val)
+      CHARACTER(LEN=32), INTENT(IN)    :: p
+      CHARACTER(LEN=*),  INTENT(IN)    :: key
+      UNSPECIFIED_TYPE,  INTENT(INOUT) :: val(*)
+    SUBROUTINE PLUMED_F_FINALIZE(p)
+      CHARACTER(LEN=32), INTENT(IN)    :: p
+\endverbatim
+
+  The main routine is "cmd", which accepts two arguments:
+  key is a string containing the name of the command
+  val is the argument. it is declared const so as to use allow passing const objects, but in practice plumed
+      is going to modify val in several cases (using a const_cast).
+  In some cases val can be omitted: just pass a NULL pointer (in C++, val is optional and can be omitted).
+  The set of possible keys is the real API of the plumed library, and will be expanded with time.
+  New commands will be added, but backward compatibility will be retained as long as possible.
+
+  To pass plumed a callback function use the following syntax (not available in FORTRAN yet)
+\verbatim
+    plumed_function_holder ff;
+    ff.p=your_function;
+    plumed_cmd(plumed,"xxxx",&ff);
+\endverbatim
+  (this is passing the your_function() function to the "xxxx" command)
+*/
+
+#ifdef __cplusplus
+ extern "C" {
+#endif
+
+/* Generic function pointer */
+typedef void (*plumed_function_pointer)(void);
+
+/**
+  \brief Holder for function pointer.
+
+  To pass plumed a callback function use the following syntax:
+\verbatim
+    plumed_function_holder ff;
+    ff.p=your_function;
+    plumed_cmd(plumed,"xxxx",&ff);
+\endverbatim
+  (this is going to pass the your_function() function to the "xxxx" command)
+*/
+
+typedef struct {
+  plumed_function_pointer p;
+} plumed_function_holder;
+
+/**
+  \brief Main plumed object
+
+  This is an object containing a Plumed instance, which should be used in
+  the MD engine. It should first be initialized with plumed_create(),
+  then it communicates with the MD engine using plumed_cmd(). Finally,
+  before the termination, it should be deallocated with plumed_finalize().
+  Its interface is very simple and general, and is expected
+  not to change across plumed versions. See \ref ReferencePlumedH.
+*/
+typedef struct {
+/**
+  \private
+  \brief Void pointer holding the real PlumedMain structure
+*/
+  void*p;
+} plumed;
+
+/** \relates plumed
+    \brief Constructor
+
+    \return The constructed plumed object
+*/
+plumed plumed_create(void);
+
+/** \relates plumed
+    \brief Tells p to execute a command
+
+    \param p The plumed object on which command is acting
+    \param key The name of the command to be executed
+    \param val The argument. It is declared as const to allow calls like plumed_cmd(p,"A","B"),
+               but for some choice of key it can change the content
+*/
+void plumed_cmd(plumed p,const char*key,const void*val);
+
+/** \relates plumed
+    \brief Destructor
+
+    \param p The plumed object to be deallocated
+*/
+void plumed_finalize(plumed p);
+
+/** \relates plumed
+    \brief Check if plumed is installed (for runtime binding)
+
+    \return 1 if plumed is installed, to 0 otherwise
+*/
+int plumed_installed(void);
+
+/** \relates plumed
+    \brief Retrieves an handler to the global structure.
+*/
+plumed plumed_global(void);
+
+/** \relates plumed
+    \brief Check if the global interface has been initialized
+
+    \return 1 if plumed has been initialized, 0 otherwise
+*/
+int plumed_ginitialized(void);
+
+/* global C interface, working on a global object */
+
+/** \relates plumed
+    \brief Constructor for the global interface.
+
+    \note Equivalent to plumed_create(), but initialize a static global plumed object
+*/
+void plumed_gcreate(void);
+
+/** \relates plumed
+    \brief Tells to the global interface to execute a command.
+
+    \param key The name of the command to be executed
+    \param val The argument. It is declared as const to allow calls like plumed_gcmd("A","B"),
+               but for some choice of key it can change the content
+
+    \note Equivalent to plumed_cmd(), but skipping the plumed argument
+*/
+void plumed_gcmd(const char* key,const void* val);
+
+/** \relates plumed
+    \brief Destructor for the global interface.
+
+    \note Equivalent to plumed_finalize(), but skipping the plumed argument
+*/
+void plumed_gfinalize(void);
+
+/* routines to convert char handler from/to plumed objects */
+
+/** \related plumed
+    \brief Converts a C handler to a FORTRAN handler
+
+    \param p The C handler
+    \param c The FORTRAN handler (a char[32])
+*/
+void   plumed_c2f(plumed p,char* c);
+
+/** \related plumed
+    \brief Converts a FORTRAN handler to a C handler
+    \param c The FORTRAN handler (a char[32])
+    \return The C handler
+*/
+plumed plumed_f2c(const char* c);
+
+#ifdef __cplusplus
+ }
+#endif
+
+#ifdef __cplusplus
+
+/* this is to include the NULL pointer */
+#include <cstdlib>
+
+/* C++ interface is hidden in PLMD namespace (same as plumed library) */
+namespace PLMD {
+
+/**
+  C++ wrapper for \ref plumed.
+
+  This class provides a C++ interface to PLUMED.
+*/
+
+class Plumed{
+  plumed main;
+/**
+   keeps track if the object was created from scratch using 
+   the defaults destructor (cloned=false) or if it was imported
+   from C or FORTRAN (cloned-true). In the latter case, the
+   plumed_finalize() method is not called when destructing the object,
+   since it is expected to be finalized in the C/FORTRAN code
+*/
+  bool cloned;
+public:
+/**
+   Check if plumed is installed (for runtime binding)
+   \return true if plumed is installed, false otherwise
+*/
+  static bool installed();
+/**
+   Check if global-plumed has been initialized
+   \return true if global plumed object (see global()) is initialized (i.e. if gcreate() has been
+           called), false otherwise.
+*/
+  static bool ginitialized();
+/**
+   Initialize global-plumed
+*/
+  static void gcreate();
+/**
+   Send a command to global-plumed
+    \param key The name of the command to be executed
+    \param val The argument. It is declared as const to allow calls like gcmd("A","B"),
+               but for some choice of key it can change the content
+*/
+  static void gcmd(const char* key,const void* val);
+/**
+   Finalize global-plumed
+*/
+  static void gfinalize();
+/**
+   Returns the Plumed global object
+   \return The Plumed global object
+*/
+  static Plumed global();
+/**
+   Constructor
+*/
+  Plumed();
+/**
+   Clone a Plumed object from a FORTRAN char* handler
+   \param c The FORTRAN handler (a char[32]).
+
+ \attention The Plumed object created in this manner
+            will not finalize the corresponding plumed structure.
+            It is expected that the FORTRAN code calls plumed_c_finalize for it
+*/
+  Plumed(const char*c);
+/**
+   Clone a Plumed object from a C plumed structure
+   \param p The C plumed structure.
+
+ \attention The Plumed object created in this manner
+            will not finalize the corresponding plumed structure.
+            It is expected that the C code calls plumed_finalize for it
+*/
+  Plumed(plumed p);
+private:
+/** Copy constructor is disabled (private and unimplemented)
+  The problem here is that after copying it will not be clear who is
+  going to finalize the corresponding plumed structure.
+*/
+  Plumed(const Plumed&);
+/** Assignment operator is disabled (private and unimplemented)
+  The problem here is that after copying it will not be clear who is
+  going to finalize the corresponding plumed structure.
+*/
+  Plumed&operator=(const Plumed&);
+public:
+/**
+   Retrieve the C plumed structure for this object
+*/
+  operator plumed()const;
+/**
+   Retrieve a FORTRAN handler for this object
+    \param c The FORTRAN handler (a char[32]).
+*/
+  void toFortran(char*c)const;
+/**
+   Send a command to this plumed object
+    \param key The name of the command to be executed
+    \param val The argument. It is declared as const to allow calls like p.cmd("A","B"),
+               but for some choice of key it can change the content
+*/
+  void cmd(const char*key,const void*val=NULL);
+/**
+   Destructor
+
+   Destructor is virtual so as to allow correct inheritance from Plumed object.
+   To avoid linking problems with g++, I specify "inline" also here (in principle
+   it should be enough to specify it down in the definition of the function, but
+   for some reason that I do not understand g++ does not inline it properly in that
+   case and complains when Plumed.h is included but Plumed.o is not linked. Anyway, the
+   way it is done here seems to work properly).
+*/
+  inline virtual ~Plumed();
+};
+
+/* All methods are inlined so as to avoid the compilation of an extra c++ file */
+
+inline
+bool Plumed::installed(){
+  return plumed_installed();
+}
+
+inline
+Plumed::Plumed():
+  main(plumed_create()),
+  cloned(false)
+{}
+
+inline
+Plumed::Plumed(const char*c):
+  main(plumed_f2c(c)),
+  cloned(true)
+{}
+
+inline
+Plumed::Plumed(plumed p):
+  main(p),
+  cloned(true)
+{}
+
+inline
+Plumed::operator plumed()const{
+  return main;
+}
+
+inline
+void Plumed::toFortran(char*c)const{
+  plumed_c2f(main,c);
+}
+
+inline
+void Plumed::cmd(const char*key,const void*val){
+  plumed_cmd(main,key,val);
+}
+
+inline
+Plumed::~Plumed(){
+  if(!cloned)plumed_finalize(main);
+}
+
+inline
+bool Plumed::ginitialized(){
+  return plumed_ginitialized();
+}
+
+inline
+void Plumed::gcreate(){
+  plumed_gcreate();
+}
+
+inline
+void Plumed::gcmd(const char* key,const void* val){
+  plumed_gcmd(key,val);
+}
+
+inline
+void Plumed::gfinalize(){
+  plumed_gfinalize();
+}
+
+inline
+Plumed Plumed::global(){
+  return plumed_global();
+}
+
+}
+
+#endif
+
+
+#endif
diff --git a/Plumed.inc b/Plumed.inc
new file mode 100644
index 0000000..cd6097a
--- /dev/null
+++ b/Plumed.inc
@@ -0,0 +1,3 @@
+# PLUMED: shared installation
+PLUMED_LOAD= /home/jas02/software/PLUMED/2.1.3-foss-2015b/lib/plumed///src/lib/libplumed.so -ldl
+PLUMED_DEPENDENCIES= /home/jas02/software/PLUMED/2.1.3-foss-2015b/lib/plumed///src/lib/libplumed.so
diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 6db37e2..cc97aa8 100644
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -32,6 +32,8 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
+
 set(LIBGROMACS_SOURCES)
 
 function (gmx_install_headers DESTINATION)
@@ -189,7 +191,7 @@ target_link_libraries(libgromacs
                       ${TNG_IO_LIBRARIES}
                       ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
                       ${XML_LIBRARIES}
-                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS})
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${PLUMED_LOAD})
 set_target_properties(libgromacs PROPERTIES
                       OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
                       SOVERSION ${LIBRARY_SOVERSION}
diff --git a/src/gromacs/CMakeLists.txt.preplumed b/src/gromacs/CMakeLists.txt.preplumed
new file mode 100644
index 0000000..6db37e2
--- /dev/null
+++ b/src/gromacs/CMakeLists.txt.preplumed
@@ -0,0 +1,232 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(LIBGROMACS_SOURCES)
+
+function (gmx_install_headers DESTINATION)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        if (DESTINATION)
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs/${DESTINATION})
+        else()
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs)
+        endif()
+        install(FILES ${ARGN} DESTINATION ${DESTINATION} COMPONENT development)
+    endif()
+endfunction ()
+
+if(GMX_USE_TNG)
+    option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
+           OFF)
+    # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
+    if(GMX_EXTERNAL_TNG)
+        find_package(TNG_IO 1.6.0)
+        if(NOT TNG_IO_FOUND)
+            message(FATAL_ERROR
+                "TNG >= 1.6.0 not found. "
+                "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
+        endif()
+        include_directories(${TNG_IO_INCLUDE_DIRS})
+    endif()
+    if(NOT GMX_EXTERNAL_TNG)
+        include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
+        tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
+        list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
+        tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+
+        if (HAVE_ZLIB)
+            list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
+            include_directories(${ZLIB_INCLUDE_DIRS})
+        endif()
+    endif()
+else()
+    # We still need to get tng/tng_io_fwd.h from somewhere!
+    include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
+endif()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(commandline)
+add_subdirectory(fft)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(random)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(timing)
+add_subdirectory(utility)
+add_subdirectory(fileio)
+add_subdirectory(swap)
+add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
+add_subdirectory(simd)
+add_subdirectory(imd)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    add_subdirectory(legacyheaders)
+    add_subdirectory(gmxana)
+    add_subdirectory(statistics)
+    add_subdirectory(analysisdata)
+    add_subdirectory(selection)
+    add_subdirectory(trajectoryanalysis)
+    add_subdirectory(tools)
+endif()
+
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES})
+
+# This would be the standard way to include thread_mpi, but
+# we want libgromacs to link the functions directly
+#if(GMX_THREAD_MPI)
+#    add_subdirectory(thread_mpi)
+#endif()
+#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
+
+tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
+list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
+
+file(GLOB LIBGROMACS_HEADERS *.h)
+configure_file(version.h.cmakein version.h)
+gmx_install_headers("" ${LIBGROMACS_HEADERS})
+gmx_install_headers("" ${CMAKE_CURRENT_BINARY_DIR}/version.h)
+
+# Add target that generates baseversion-gen.c every time make is run
+# if git version info is requested, or create it statically.
+# This code is here instead of utility/CMakeLists.txt because CMake
+# ignores set_source_file_properties from subdirectories.
+set(GENERATED_VERSION_FILE
+    ${CMAKE_CURRENT_BINARY_DIR}/utility/baseversion-gen.c)
+set(GENERATED_VERSION_FILE_SOURCE
+    ${CMAKE_CURRENT_SOURCE_DIR}/utility/baseversion-gen.c.cmakein)
+if (GMX_GIT_VERSION_INFO)
+    add_custom_target(gmx-version ALL
+            COMMAND ${CMAKE_COMMAND}
+                -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
+                -D PROJECT_VERSION="${PROJECT_VERSION}"
+                -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
+                -D VERSION_CMAKEIN=${GENERATED_VERSION_FILE_SOURCE}
+                -D VERSION_OUT=${GENERATED_VERSION_FILE}
+                -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
+            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            DEPENDS ${GENERATED_VERSION_FILE_SOURCE}
+            COMMENT "Generating git version information")
+    set_source_files_properties(${GENERATED_VERSION_FILE}
+                                PROPERTIES GENERATED true)
+else()
+    set(GMX_PROJECT_VERSION_STR ${PROJECT_VERSION})
+    configure_file(${GENERATED_VERSION_FILE_SOURCE} ${GENERATED_VERSION_FILE})
+endif()
+list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
+
+# apply gcc 4.4.x bug workaround
+if(GMX_USE_GCC44_BUG_WORKAROUND)
+   include(gmxGCC44O3BugWorkaround)
+   gmx_apply_gcc44_bug_workaround("gmxlib/bondfree.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/force.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
+endif()
+
+add_library(libgromacs ${LIBGROMACS_SOURCES})
+if (GMX_GIT_VERSION_INFO)
+    add_dependencies(libgromacs gmx-version)
+endif()
+
+# Recent versions of gcc and clang give warnings on scanner.cpp, which
+# is a generated source file. These are awkward to suppress inline, so
+# we do it in the compilation command (after testing that the compiler
+# supports the suppressions). Setting the properties only works after
+# the related target has been created, e.g. after when the file is
+# used with add_library().
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
+if (HAS_NO_UNUSED_PARAMETER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
+endif()
+check_cxx_compiler_flag(-Wno-deprecated-register HAS_NO_DEPRECATED_REGISTER)
+if (HAS_NO_DEPRECATED_REGISTER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated-register")
+else()
+    check_cxx_compiler_flag(-Wno-deprecated HAS_NO_DEPRECATED)
+    if (HAS_NO_DEPRECATED)
+        set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated")
+    endif()
+endif()
+set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
+
+target_link_libraries(libgromacs
+                      ${EXTRAE_LIBRARIES}
+                      ${GMX_GPU_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${TNG_IO_LIBRARIES}
+                      ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
+                      ${XML_LIBRARIES}
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS})
+set_target_properties(libgromacs PROPERTIES
+                      OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+                      SOVERSION ${LIBRARY_SOVERSION}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+# Only install the library in mdrun-only mode if it is actually necessary
+# for the binary
+if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
+    install(TARGETS libgromacs
+        LIBRARY DESTINATION ${LIB_INSTALL_DIR}
+        RUNTIME DESTINATION ${BIN_INSTALL_DIR}
+        ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+        COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgromacs.pc.cmakein
+                   ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc @ONLY)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
+            DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+            RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
+            COMPONENT development)
+endif()
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_GPU)
+        foreach(CUDA_LIB ${CUDA_LIBRARIES})
+            string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+            if(IS_CUDART) #libcuda should not be installed
+                #install also name-links (linker uses those)
+                file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+                install(FILES ${CUDA_LIBS} DESTINATION
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif()
diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 5230983..8227d5b 100644
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -67,6 +67,14 @@
 #include "gromacs/timing/wallcycle.h"
 #include "gmx_fatal.h"
 
+/* PLUMED */
+#include "../../../Plumed.h"
+int    plumedswitch=0;
+plumed plumedmain;
+void(*plumedcmd)(plumed,const char*,const void*)=NULL;
+/* END PLUMED */
+
+
 void ns(FILE              *fp,
         t_forcerec        *fr,
         matrix             box,
@@ -737,6 +745,13 @@ void do_force_lowlevel(FILE       *fplog,   gmx_int64_t step,
         pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
     }
 
+    /* PLUMED */
+    if(plumedswitch){
+      int plumedNeedsEnergy;
+      (*plumedcmd)(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+      if(!plumedNeedsEnergy) (*plumedcmd)(plumedmain,"performCalc",NULL);
+    }
+    /* END PLUMED */
 }
 
 void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
diff --git a/src/gromacs/mdlib/force.c.preplumed b/src/gromacs/mdlib/force.c.preplumed
new file mode 100644
index 0000000..5230983
--- /dev/null
+++ b/src/gromacs/mdlib/force.c.preplumed
@@ -0,0 +1,1018 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "macros.h"
+#include "physics.h"
+#include "force.h"
+#include "nonbonded.h"
+#include "names.h"
+#include "network.h"
+#include "pbc.h"
+#include "ns.h"
+#include "nrnb.h"
+#include "bondf.h"
+#include "mshift.h"
+#include "txtdump.h"
+#include "coulomb.h"
+#include "pme.h"
+#include "mdrun.h"
+#include "domdec.h"
+#include "qmmm.h"
+#include "gmx_omp_nthreads.h"
+
+#include "gromacs/timing/wallcycle.h"
+#include "gmx_fatal.h"
+
+void ns(FILE              *fp,
+        t_forcerec        *fr,
+        matrix             box,
+        gmx_groups_t      *groups,
+        gmx_localtop_t    *top,
+        t_mdatoms         *md,
+        t_commrec         *cr,
+        t_nrnb            *nrnb,
+        gmx_bool           bFillGrid,
+        gmx_bool           bDoLongRangeNS)
+{
+    char   *ptr;
+    int     nsearch;
+
+
+    if (!fr->ns.nblist_initialized)
+    {
+        init_neighbor_list(fp, fr, md->homenr);
+    }
+
+    if (fr->bTwinRange)
+    {
+        fr->nlr = 0;
+    }
+
+    nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
+                                bFillGrid, bDoLongRangeNS);
+    if (debug)
+    {
+        fprintf(debug, "nsearch = %d\n", nsearch);
+    }
+
+    /* Check whether we have to do dynamic load balancing */
+    /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
+       count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
+       &(top->idef),opts->ngener);
+     */
+    if (fr->ns.dump_nl > 0)
+    {
+        dump_nblist(fp, cr, fr, fr->ns.dump_nl);
+    }
+}
+
+static void reduce_thread_forces(int n, rvec *f,
+                                 tensor vir_q, tensor vir_lj,
+                                 real *Vcorr_q, real *Vcorr_lj,
+                                 real *dvdl_q, real *dvdl_lj,
+                                 int nthreads, f_thread_t *f_t)
+{
+    int t, i;
+    int nthreads_loop gmx_unused;
+
+    /* This reduction can run over any number of threads */
+    nthreads_loop = gmx_omp_nthreads_get(emntBonded);
+#pragma omp parallel for num_threads(nthreads_loop) private(t) schedule(static)
+    for (i = 0; i < n; i++)
+    {
+        for (t = 1; t < nthreads; t++)
+        {
+            rvec_inc(f[i], f_t[t].f[i]);
+        }
+    }
+    for (t = 1; t < nthreads; t++)
+    {
+        *Vcorr_q  += f_t[t].Vcorr_q;
+        *Vcorr_lj += f_t[t].Vcorr_lj;
+        *dvdl_q   += f_t[t].dvdl[efptCOUL];
+        *dvdl_lj  += f_t[t].dvdl[efptVDW];
+        m_add(vir_q, f_t[t].vir_q, vir_q);
+        m_add(vir_lj, f_t[t].vir_lj, vir_lj);
+    }
+}
+
+void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
+{
+    fprintf(fplog, "  %-30s V %12.5e  dVdl %12.5e\n", s, v, dvdlambda);
+}
+
+void do_force_lowlevel(FILE       *fplog,   gmx_int64_t step,
+                       t_forcerec *fr,      t_inputrec *ir,
+                       t_idef     *idef,    t_commrec  *cr,
+                       t_nrnb     *nrnb,    gmx_wallcycle_t wcycle,
+                       t_mdatoms  *md,
+                       rvec       x[],      history_t  *hist,
+                       rvec       f[],
+                       rvec       f_longrange[],
+                       gmx_enerdata_t *enerd,
+                       t_fcdata   *fcd,
+                       gmx_localtop_t *top,
+                       gmx_genborn_t *born,
+                       t_atomtypes *atype,
+                       gmx_bool       bBornRadii,
+                       matrix     box,
+                       t_lambda   *fepvals,
+                       real       *lambda,
+                       t_graph    *graph,
+                       t_blocka   *excl,
+                       rvec       mu_tot[],
+                       int        flags,
+                       float      *cycles_pme)
+{
+    int         i, j;
+    int         donb_flags;
+    gmx_bool    bDoEpot, bSepDVDL, bSB;
+    int         pme_flags;
+    matrix      boxs;
+    rvec        box_size;
+    t_pbc       pbc;
+    char        buf[22];
+    double      clam_i, vlam_i;
+    real        dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
+    real        dvdl_q, dvdl_lj;
+
+#ifdef GMX_MPI
+    double  t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
+#endif
+
+#define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
+
+    set_pbc(&pbc, fr->ePBC, box);
+
+    /* reset free energy components */
+    for (i = 0; i < efptNR; i++)
+    {
+        dvdl_nb[i]  = 0;
+        dvdl_dum[i] = 0;
+    }
+
+    /* Reset box */
+    for (i = 0; (i < DIM); i++)
+    {
+        box_size[i] = box[i][i];
+    }
+
+    bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
+    debug_gmx();
+
+    /* do QMMM first if requested */
+    if (fr->bQMMM)
+    {
+        enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
+    }
+
+    if (bSepDVDL)
+    {
+        fprintf(fplog, "Step %s: non-bonded V and dVdl for rank %d:\n",
+                gmx_step_str(step, buf), cr->nodeid);
+    }
+
+    /* Call the short range functions all in one go. */
+
+#ifdef GMX_MPI
+    /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
+#define TAKETIME FALSE
+    if (TAKETIME)
+    {
+        MPI_Barrier(cr->mpi_comm_mygroup);
+        t0 = MPI_Wtime();
+    }
+#endif
+
+    if (ir->nwall)
+    {
+        /* foreign lambda component for walls */
+        real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
+                                   enerd->grpp.ener[egLJSR], nrnb);
+        PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
+        enerd->dvdl_lin[efptVDW] += dvdl_walls;
+    }
+
+    /* If doing GB, reset dvda and calculate the Born radii */
+    if (ir->implicit_solvent)
+    {
+        wallcycle_sub_start(wcycle, ewcsNONBONDED);
+
+        for (i = 0; i < born->nr; i++)
+        {
+            fr->dvda[i] = 0;
+        }
+
+        if (bBornRadii)
+        {
+            calc_gb_rad(cr, fr, ir, top, x, &(fr->gblist), born, md, nrnb);
+        }
+
+        wallcycle_sub_stop(wcycle, ewcsNONBONDED);
+    }
+
+    where();
+    /* We only do non-bonded calculation with group scheme here, the verlet
+     * calls are done from do_force_cutsVERLET(). */
+    if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
+    {
+        donb_flags = 0;
+        /* Add short-range interactions */
+        donb_flags |= GMX_NONBONDED_DO_SR;
+
+        /* Currently all group scheme kernels always calculate (shift-)forces */
+        if (flags & GMX_FORCE_FORCES)
+        {
+            donb_flags |= GMX_NONBONDED_DO_FORCE;
+        }
+        if (flags & GMX_FORCE_VIRIAL)
+        {
+            donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
+        }
+        if (flags & GMX_FORCE_ENERGY)
+        {
+            donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
+        }
+        if (flags & GMX_FORCE_DO_LR)
+        {
+            donb_flags |= GMX_NONBONDED_DO_LR;
+        }
+
+        wallcycle_sub_start(wcycle, ewcsNONBONDED);
+        do_nonbonded(fr, x, f, f_longrange, md, excl,
+                     &enerd->grpp, nrnb,
+                     lambda, dvdl_nb, -1, -1, donb_flags);
+
+        /* If we do foreign lambda and we have soft-core interactions
+         * we have to recalculate the (non-linear) energies contributions.
+         */
+        if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
+        {
+            for (i = 0; i < enerd->n_lambda; i++)
+            {
+                for (j = 0; j < efptNR; j++)
+                {
+                    lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
+                }
+                reset_foreign_enerdata(enerd);
+                do_nonbonded(fr, x, f, f_longrange, md, excl,
+                             &(enerd->foreign_grpp), nrnb,
+                             lam_i, dvdl_dum, -1, -1,
+                             (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
+                sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
+                enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
+            }
+        }
+        wallcycle_sub_stop(wcycle, ewcsNONBONDED);
+        where();
+    }
+
+    /* If we are doing GB, calculate bonded forces and apply corrections
+     * to the solvation forces */
+    /* MRS: Eventually, many need to include free energy contribution here! */
+    if (ir->implicit_solvent)
+    {
+        wallcycle_sub_start(wcycle, ewcsBONDED);
+        calc_gb_forces(cr, md, born, top, x, f, fr, idef,
+                       ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
+        wallcycle_sub_stop(wcycle, ewcsBONDED);
+    }
+
+#ifdef GMX_MPI
+    if (TAKETIME)
+    {
+        t1          = MPI_Wtime();
+        fr->t_fnbf += t1-t0;
+    }
+#endif
+
+    if (fepvals->sc_alpha != 0)
+    {
+        enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
+    }
+    else
+    {
+        enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
+    }
+
+    if (fepvals->sc_alpha != 0)
+
+    /* even though coulomb part is linear, we already added it, beacuse we
+       need to go through the vdw calculation anyway */
+    {
+        enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
+    }
+    else
+    {
+        enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
+    }
+
+    if (bSepDVDL)
+    {
+        real V_short_range    = 0;
+        real dvdl_short_range = 0;
+
+        for (i = 0; i < enerd->grpp.nener; i++)
+        {
+            V_short_range +=
+                (fr->bBHAM ?
+                 enerd->grpp.ener[egBHAMSR][i] :
+                 enerd->grpp.ener[egLJSR][i])
+                + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
+        }
+        dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
+        PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
+                      V_short_range,
+                      dvdl_short_range);
+    }
+    debug_gmx();
+
+
+    if (debug)
+    {
+        pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
+    }
+
+    /* Shift the coordinates. Must be done before bonded forces and PPPM,
+     * but is also necessary for SHAKE and update, therefore it can NOT
+     * go when no bonded forces have to be evaluated.
+     */
+
+    /* Here sometimes we would not need to shift with NBFonly,
+     * but we do so anyhow for consistency of the returned coordinates.
+     */
+    if (graph)
+    {
+        shift_self(graph, box, x);
+        if (TRICLINIC(box))
+        {
+            inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
+        }
+        else
+        {
+            inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
+        }
+    }
+    /* Check whether we need to do bondeds or correct for exclusions */
+    if (fr->bMolPBC &&
+        ((flags & GMX_FORCE_BONDED)
+         || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
+    {
+        /* Since all atoms are in the rectangular or triclinic unit-cell,
+         * only single box vector shifts (2 in x) are required.
+         */
+        set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
+    }
+    debug_gmx();
+
+    if (flags & GMX_FORCE_BONDED)
+    {
+        wallcycle_sub_start(wcycle, ewcsBONDED);
+        calc_bonds(fplog, cr->ms,
+                   idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
+                   DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
+                   flags,
+                   fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
+
+        /* Check if we have to determine energy differences
+         * at foreign lambda's.
+         */
+        if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
+            idef->ilsort != ilsortNO_FE)
+        {
+            if (idef->ilsort != ilsortFE_SORTED)
+            {
+                gmx_incons("The bonded interactions are not sorted for free energy");
+            }
+            for (i = 0; i < enerd->n_lambda; i++)
+            {
+                reset_foreign_enerdata(enerd);
+                for (j = 0; j < efptNR; j++)
+                {
+                    lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
+                }
+                calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
+                                  fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+                sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
+                enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
+            }
+        }
+        debug_gmx();
+
+        wallcycle_sub_stop(wcycle, ewcsBONDED);
+    }
+
+    where();
+
+    *cycles_pme = 0;
+    if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
+    {
+        real Vlr             = 0, Vcorr = 0;
+        real dvdl_long_range = 0;
+        int  status          = 0;
+
+        bSB = (ir->nwall == 2);
+        if (bSB)
+        {
+            copy_mat(box, boxs);
+            svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
+            box_size[ZZ] *= ir->wall_ewald_zfac;
+        }
+    }
+
+    /* Do long-range electrostatics and/or LJ-PME, including related short-range
+     * corrections.
+     */
+
+    clear_mat(fr->vir_el_recip);
+    clear_mat(fr->vir_lj_recip);
+
+    if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
+    {
+        real Vlr_q             = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
+        real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
+        int  status            = 0;
+
+        if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
+        {
+            real dvdl_long_range_correction_q   = 0;
+            real dvdl_long_range_correction_lj  = 0;
+            /* With the Verlet scheme exclusion forces are calculated
+             * in the non-bonded kernel.
+             */
+            /* The TPI molecule does not have exclusions with the rest
+             * of the system and no intra-molecular PME grid
+             * contributions will be calculated in
+             * gmx_pme_calc_energy.
+             */
+            if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
+                ir->ewald_geometry != eewg3D ||
+                ir->epsilon_surface != 0)
+            {
+                int nthreads, t;
+
+                wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
+
+                if (fr->n_tpi > 0)
+                {
+                    gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
+                }
+
+                nthreads = gmx_omp_nthreads_get(emntBonded);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+                for (t = 0; t < nthreads; t++)
+                {
+                    int     s, e, i;
+                    rvec   *fnv;
+                    tensor *vir_q, *vir_lj;
+                    real   *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
+                    if (t == 0)
+                    {
+                        fnv       = fr->f_novirsum;
+                        vir_q     = &fr->vir_el_recip;
+                        vir_lj    = &fr->vir_lj_recip;
+                        Vcorrt_q  = &Vcorr_q;
+                        Vcorrt_lj = &Vcorr_lj;
+                        dvdlt_q   = &dvdl_long_range_correction_q;
+                        dvdlt_lj  = &dvdl_long_range_correction_lj;
+                    }
+                    else
+                    {
+                        fnv       = fr->f_t[t].f;
+                        vir_q     = &fr->f_t[t].vir_q;
+                        vir_lj    = &fr->f_t[t].vir_lj;
+                        Vcorrt_q  = &fr->f_t[t].Vcorr_q;
+                        Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
+                        dvdlt_q   = &fr->f_t[t].dvdl[efptCOUL];
+                        dvdlt_lj  = &fr->f_t[t].dvdl[efptVDW];
+                        for (i = 0; i < fr->natoms_force; i++)
+                        {
+                            clear_rvec(fnv[i]);
+                        }
+                        clear_mat(*vir_q);
+                        clear_mat(*vir_lj);
+                    }
+                    *dvdlt_q  = 0;
+                    *dvdlt_lj = 0;
+
+                    ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
+                                       cr, t, fr,
+                                       md->chargeA, md->chargeB,
+                                       md->sqrt_c6A, md->sqrt_c6B,
+                                       md->sigmaA, md->sigmaB,
+                                       md->sigma3A, md->sigma3B,
+                                       md->nChargePerturbed || md->nTypePerturbed,
+                                       ir->cutoff_scheme != ecutsVERLET,
+                                       excl, x, bSB ? boxs : box, mu_tot,
+                                       ir->ewald_geometry,
+                                       ir->epsilon_surface,
+                                       fnv, *vir_q, *vir_lj,
+                                       Vcorrt_q, Vcorrt_lj,
+                                       lambda[efptCOUL], lambda[efptVDW],
+                                       dvdlt_q, dvdlt_lj);
+                }
+                if (nthreads > 1)
+                {
+                    reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
+                                         fr->vir_el_recip, fr->vir_lj_recip,
+                                         &Vcorr_q, &Vcorr_lj,
+                                         &dvdl_long_range_correction_q,
+                                         &dvdl_long_range_correction_lj,
+                                         nthreads, fr->f_t);
+                }
+                wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
+            }
+
+            if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
+            {
+                Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
+                                                   &dvdl_long_range_correction_q,
+                                                   fr->vir_el_recip);
+            }
+
+            PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
+            PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
+            enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
+            enerd->dvdl_lin[efptVDW]  += dvdl_long_range_correction_lj;
+        }
+
+        if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)))
+        {
+            if (cr->duty & DUTY_PME)
+            {
+                /* Do reciprocal PME for Coulomb and/or LJ. */
+                assert(fr->n_tpi >= 0);
+                if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
+                {
+                    pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
+                    if (EEL_PME(fr->eeltype))
+                    {
+                        pme_flags     |= GMX_PME_DO_COULOMB;
+                    }
+                    if (EVDW_PME(fr->vdwtype))
+                    {
+                        pme_flags |= GMX_PME_DO_LJ;
+                    }
+                    if (flags & GMX_FORCE_FORCES)
+                    {
+                        pme_flags |= GMX_PME_CALC_F;
+                    }
+                    if (flags & GMX_FORCE_VIRIAL)
+                    {
+                        pme_flags |= GMX_PME_CALC_ENER_VIR;
+                    }
+                    if (fr->n_tpi > 0)
+                    {
+                        /* We don't calculate f, but we do want the potential */
+                        pme_flags |= GMX_PME_CALC_POT;
+                    }
+                    wallcycle_start(wcycle, ewcPMEMESH);
+                    status = gmx_pme_do(fr->pmedata,
+                                        0, md->homenr - fr->n_tpi,
+                                        x, fr->f_novirsum,
+                                        md->chargeA, md->chargeB,
+                                        md->sqrt_c6A, md->sqrt_c6B,
+                                        md->sigmaA, md->sigmaB,
+                                        bSB ? boxs : box, cr,
+                                        DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
+                                        DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
+                                        nrnb, wcycle,
+                                        fr->vir_el_recip, fr->ewaldcoeff_q,
+                                        fr->vir_lj_recip, fr->ewaldcoeff_lj,
+                                        &Vlr_q, &Vlr_lj,
+                                        lambda[efptCOUL], lambda[efptVDW],
+                                        &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
+                    *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
+                    if (status != 0)
+                    {
+                        gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
+                    }
+                    /* We should try to do as little computation after
+                     * this as possible, because parallel PME synchronizes
+                     * the nodes, so we want all load imbalance of the
+                     * rest of the force calculation to be before the PME
+                     * call.  DD load balancing is done on the whole time
+                     * of the force call (without PME).
+                     */
+                }
+                if (fr->n_tpi > 0)
+                {
+                    if (EVDW_PME(ir->vdwtype))
+                    {
+
+                        gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
+                    }
+                    /* Determine the PME grid energy of the test molecule
+                     * with the PME grid potential of the other charges.
+                     */
+                    gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
+                                        x + md->homenr - fr->n_tpi,
+                                        md->chargeA + md->homenr - fr->n_tpi,
+                                        &Vlr_q);
+                }
+                PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
+            }
+        }
+
+        if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
+        {
+            Vlr_q = do_ewald(ir, x, fr->f_novirsum,
+                             md->chargeA, md->chargeB,
+                             box_size, cr, md->homenr,
+                             fr->vir_el_recip, fr->ewaldcoeff_q,
+                             lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
+            PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
+        }
+
+        /* Note that with separate PME nodes we get the real energies later */
+        enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
+        enerd->dvdl_lin[efptVDW]  += dvdl_long_range_lj;
+        enerd->term[F_COUL_RECIP]  = Vlr_q + Vcorr_q;
+        enerd->term[F_LJ_RECIP]    = Vlr_lj + Vcorr_lj;
+        if (debug)
+        {
+            fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
+                    Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
+            pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
+            pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
+            fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
+                    Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
+            pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
+        }
+    }
+    else
+    {
+        /* Is there a reaction-field exclusion correction needed? */
+        if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
+        {
+            /* With the Verlet scheme, exclusion forces are calculated
+             * in the non-bonded kernel.
+             */
+            if (ir->cutoff_scheme != ecutsVERLET)
+            {
+                real dvdl_rf_excl      = 0;
+                enerd->term[F_RF_EXCL] =
+                    RF_excl_correction(fr, graph, md, excl, x, f,
+                                       fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
+
+                enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
+                PRINT_SEPDVDL("RF exclusion correction",
+                              enerd->term[F_RF_EXCL], dvdl_rf_excl);
+            }
+        }
+    }
+    where();
+    debug_gmx();
+
+    if (debug)
+    {
+        print_nrnb(debug, nrnb);
+    }
+    debug_gmx();
+
+#ifdef GMX_MPI
+    if (TAKETIME)
+    {
+        t2 = MPI_Wtime();
+        MPI_Barrier(cr->mpi_comm_mygroup);
+        t3          = MPI_Wtime();
+        fr->t_wait += t3-t2;
+        if (fr->timesteps == 11)
+        {
+            fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
+                    cr->nodeid, gmx_step_str(fr->timesteps, buf),
+                    100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
+                    (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
+        }
+        fr->timesteps++;
+    }
+#endif
+
+    if (debug)
+    {
+        pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
+    }
+
+}
+
+void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
+{
+    int i, n2;
+
+    for (i = 0; i < F_NRE; i++)
+    {
+        enerd->term[i]         = 0;
+        enerd->foreign_term[i] = 0;
+    }
+
+
+    for (i = 0; i < efptNR; i++)
+    {
+        enerd->dvdl_lin[i]     = 0;
+        enerd->dvdl_nonlin[i]  = 0;
+    }
+
+    n2 = ngener*ngener;
+    if (debug)
+    {
+        fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
+    }
+    enerd->grpp.nener         = n2;
+    enerd->foreign_grpp.nener = n2;
+    for (i = 0; (i < egNR); i++)
+    {
+        snew(enerd->grpp.ener[i], n2);
+        snew(enerd->foreign_grpp.ener[i], n2);
+    }
+
+    if (n_lambda)
+    {
+        enerd->n_lambda = 1 + n_lambda;
+        snew(enerd->enerpart_lambda, enerd->n_lambda);
+    }
+    else
+    {
+        enerd->n_lambda = 0;
+    }
+}
+
+void destroy_enerdata(gmx_enerdata_t *enerd)
+{
+    int i;
+
+    for (i = 0; (i < egNR); i++)
+    {
+        sfree(enerd->grpp.ener[i]);
+    }
+
+    for (i = 0; (i < egNR); i++)
+    {
+        sfree(enerd->foreign_grpp.ener[i]);
+    }
+
+    if (enerd->n_lambda)
+    {
+        sfree(enerd->enerpart_lambda);
+    }
+}
+
+static real sum_v(int n, real v[])
+{
+    real t;
+    int  i;
+
+    t = 0.0;
+    for (i = 0; (i < n); i++)
+    {
+        t = t + v[i];
+    }
+
+    return t;
+}
+
+void sum_epot(gmx_grppairener_t *grpp, real *epot)
+{
+    int i;
+
+    /* Accumulate energies */
+    epot[F_COUL_SR]  = sum_v(grpp->nener, grpp->ener[egCOULSR]);
+    epot[F_LJ]       = sum_v(grpp->nener, grpp->ener[egLJSR]);
+    epot[F_LJ14]     = sum_v(grpp->nener, grpp->ener[egLJ14]);
+    epot[F_COUL14]   = sum_v(grpp->nener, grpp->ener[egCOUL14]);
+    epot[F_COUL_LR]  = sum_v(grpp->nener, grpp->ener[egCOULLR]);
+    epot[F_LJ_LR]    = sum_v(grpp->nener, grpp->ener[egLJLR]);
+    /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
+    epot[F_GBPOL]   += sum_v(grpp->nener, grpp->ener[egGB]);
+
+/* lattice part of LR doesnt belong to any group
+ * and has been added earlier
+ */
+    epot[F_BHAM]     = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
+    epot[F_BHAM_LR]  = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
+
+    epot[F_EPOT] = 0;
+    for (i = 0; (i < F_EPOT); i++)
+    {
+        if (i != F_DISRESVIOL && i != F_ORIRESDEV)
+        {
+            epot[F_EPOT] += epot[i];
+        }
+    }
+}
+
+void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
+{
+    int    i, j, index;
+    double dlam;
+
+    enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW];  /* include dispersion correction */
+    enerd->term[F_DVDL]       = 0.0;
+    for (i = 0; i < efptNR; i++)
+    {
+        if (fepvals->separate_dvdl[i])
+        {
+            /* could this be done more readably/compactly? */
+            switch (i)
+            {
+                case (efptMASS):
+                    index = F_DKDL;
+                    break;
+                case (efptCOUL):
+                    index = F_DVDL_COUL;
+                    break;
+                case (efptVDW):
+                    index = F_DVDL_VDW;
+                    break;
+                case (efptBONDED):
+                    index = F_DVDL_BONDED;
+                    break;
+                case (efptRESTRAINT):
+                    index = F_DVDL_RESTRAINT;
+                    break;
+                default:
+                    index = F_DVDL;
+                    break;
+            }
+            enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
+            if (debug)
+            {
+                fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
+                        efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+            }
+        }
+        else
+        {
+            enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
+            if (debug)
+            {
+                fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
+                        efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+            }
+        }
+    }
+
+    /* Notes on the foreign lambda free energy difference evaluation:
+     * Adding the potential and ekin terms that depend linearly on lambda
+     * as delta lam * dvdl to the energy differences is exact.
+     * For the constraints this is not exact, but we have no other option
+     * without literally changing the lengths and reevaluating the energies at each step.
+     * (try to remedy this post 4.6 - MRS)
+     * For the non-bonded LR term we assume that the soft-core (if present)
+     * no longer affects the energy beyond the short-range cut-off,
+     * which is a very good approximation (except for exotic settings).
+     * (investigate how to overcome this post 4.6 - MRS)
+     */
+    if (fepvals->separate_dvdl[efptBONDED])
+    {
+        enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
+    }
+    else
+    {
+        enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
+    }
+    enerd->term[F_DVDL_CONSTR] = 0;
+
+    for (i = 0; i < fepvals->n_lambda; i++)
+    {
+        /* note we are iterating over fepvals here!
+           For the current lam, dlam = 0 automatically,
+           so we don't need to add anything to the
+           enerd->enerpart_lambda[0] */
+
+        /* we don't need to worry about dvdl_lin contributions to dE at
+           current lambda, because the contributions to the current
+           lambda are automatically zeroed */
+
+        for (j = 0; j < efptNR; j++)
+        {
+            /* Note that this loop is over all dhdl components, not just the separated ones */
+            dlam = (fepvals->all_lambda[j][i]-lambda[j]);
+            enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
+            if (debug)
+            {
+                fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
+                        fepvals->all_lambda[j][i], efpt_names[j],
+                        (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
+                        dlam, enerd->dvdl_lin[j]);
+            }
+        }
+    }
+}
+
+
+void reset_foreign_enerdata(gmx_enerdata_t *enerd)
+{
+    int  i, j;
+
+    /* First reset all foreign energy components.  Foreign energies always called on
+       neighbor search steps */
+    for (i = 0; (i < egNR); i++)
+    {
+        for (j = 0; (j < enerd->grpp.nener); j++)
+        {
+            enerd->foreign_grpp.ener[i][j] = 0.0;
+        }
+    }
+
+    /* potential energy components */
+    for (i = 0; (i <= F_EPOT); i++)
+    {
+        enerd->foreign_term[i] = 0.0;
+    }
+}
+
+void reset_enerdata(t_forcerec *fr, gmx_bool bNS,
+                    gmx_enerdata_t *enerd,
+                    gmx_bool bMaster)
+{
+    gmx_bool bKeepLR;
+    int      i, j;
+
+    /* First reset all energy components, except for the long range terms
+     * on the master at non neighbor search steps, since the long range
+     * terms have already been summed at the last neighbor search step.
+     */
+    bKeepLR = (fr->bTwinRange && !bNS);
+    for (i = 0; (i < egNR); i++)
+    {
+        if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
+        {
+            for (j = 0; (j < enerd->grpp.nener); j++)
+            {
+                enerd->grpp.ener[i][j] = 0.0;
+            }
+        }
+    }
+    for (i = 0; i < efptNR; i++)
+    {
+        enerd->dvdl_lin[i]    = 0.0;
+        enerd->dvdl_nonlin[i] = 0.0;
+    }
+
+    /* Normal potential energy components */
+    for (i = 0; (i <= F_EPOT); i++)
+    {
+        enerd->term[i] = 0.0;
+    }
+    /* Initialize the dVdlambda term with the long range contribution */
+    /* Initialize the dvdl term with the long range contribution */
+    enerd->term[F_DVDL]            = 0.0;
+    enerd->term[F_DVDL_COUL]       = 0.0;
+    enerd->term[F_DVDL_VDW]        = 0.0;
+    enerd->term[F_DVDL_BONDED]     = 0.0;
+    enerd->term[F_DVDL_RESTRAINT]  = 0.0;
+    enerd->term[F_DKDL]            = 0.0;
+    if (enerd->n_lambda > 0)
+    {
+        for (i = 0; i < enerd->n_lambda; i++)
+        {
+            enerd->enerpart_lambda[i] = 0.0;
+        }
+    }
+    /* reset foreign energy data - separate function since we also call it elsewhere */
+    reset_foreign_enerdata(enerd);
+}
diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 69008f5..5114fa0 100644
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -80,6 +80,13 @@
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/imd/imd.h"
 
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+extern void(*plumedcmd)(plumed,const char*,const void*);
+/* END PLUMED */
+
 typedef struct {
     t_state  s;
     rvec    *f;
@@ -442,6 +449,43 @@ void init_em(FILE *fplog, const char *title,
 
     clear_rvec(mu_tot);
     calc_shifts(ems->s.box, fr->shift_vec);
+
+    /* PLUMED */
+    if(plumedswitch){
+      if(cr->ms && cr->ms->nsim>1) {
+        if(MASTER(cr)) (*plumedcmd) (plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
+        if(PAR(cr)){
+          if(DOMAINDECOMP(cr)) {
+            (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
+          }else{
+            (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
+          }
+        }
+        (*plumedcmd) (plumedmain,"GREX init",NULL);
+      }
+      if(PAR(cr)){
+        if(DOMAINDECOMP(cr)) {
+          (*plumedcmd) (plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+        }else{
+          (*plumedcmd) (plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
+        }
+      }
+      (*plumedcmd) (plumedmain,"setNatoms",&top_global->natoms);
+      (*plumedcmd) (plumedmain,"setMDEngine","gromacs");
+      (*plumedcmd) (plumedmain,"setLog",fplog);
+      real real_delta_t;
+      real_delta_t=ir->delta_t;
+      (*plumedcmd) (plumedmain,"setTimestep",&real_delta_t);
+      (*plumedcmd) (plumedmain,"init",NULL);
+
+      if(PAR(cr)){
+        if(DOMAINDECOMP(cr)) {
+          (*plumedcmd) (plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+          (*plumedcmd) (plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+        }
+      }
+    }
+    /* END PLUMED */
 }
 
 static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
@@ -737,12 +781,34 @@ static void evaluate_energy(FILE *fplog, t_commrec *cr,
         em_dd_partition_system(fplog, count, cr, top_global, inputrec,
                                ems, top, mdatoms, fr, vsite, constr,
                                nrnb, wcycle);
+        /* PLUMED */
+        if(plumedswitch){
+          (*plumedcmd) (plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+          (*plumedcmd) (plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+        }
+        /* END PLUMED */
     }
 
     /* Calc force & energy on new trial position  */
     /* do_force always puts the charge groups in the box and shifts again
      * We do not unshift, so molecules are always whole in congrad.c
      */
+    /* PLUMED */
+    int plumedNeedsEnergy=0;
+    matrix plumed_vir;
+    if(plumedswitch){
+      long int lstep=count; (*plumedcmd)(plumedmain,"setStepLong",&count);
+      (*plumedcmd) (plumedmain,"setPositions",&ems->s.x[0][0]);
+      (*plumedcmd) (plumedmain,"setMasses",&mdatoms->massT[0]);
+      (*plumedcmd) (plumedmain,"setCharges",&mdatoms->chargeA[0]);
+      (*plumedcmd) (plumedmain,"setBox",&ems->s.box[0][0]);
+      (*plumedcmd) (plumedmain,"prepareCalc",NULL);
+      (*plumedcmd) (plumedmain,"setForces",&ems->f[0][0]);
+      (*plumedcmd) (plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+      clear_mat(plumed_vir);
+      (*plumedcmd) (plumedmain,"setVirial",&plumed_vir[0][0]);
+    }
+    /* END PLUMED */
     do_force(fplog, cr, inputrec,
              count, nrnb, wcycle, top, &top_global->groups,
              ems->s.box, ems->s.x, &ems->s.hist,
@@ -751,6 +817,19 @@ static void evaluate_energy(FILE *fplog, t_commrec *cr,
              GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
              GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
              (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
+    /* PLUMED */
+    if(plumedswitch){
+      if(plumedNeedsEnergy) {
+        msmul(force_vir,2.0,plumed_vir);
+        (*plumedcmd) (plumedmain,"setEnergy",&enerd->term[F_EPOT]);
+        (*plumedcmd) (plumedmain,"performCalc",NULL);
+        msmul(plumed_vir,0.5,force_vir);
+      } else {
+        msmul(plumed_vir,0.5,plumed_vir);
+        m_add(force_vir,plumed_vir,force_vir);
+      }
+    }
+    /* END PLUMED */
 
     /* Clear the unused shake virial and pressure */
     clear_mat(shake_vir);
diff --git a/src/gromacs/mdlib/minimize.c.preplumed b/src/gromacs/mdlib/minimize.c.preplumed
new file mode 100644
index 0000000..69008f5
--- /dev/null
+++ b/src/gromacs/mdlib/minimize.c.preplumed
@@ -0,0 +1,2906 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <string.h>
+#include <time.h>
+#include <math.h>
+#include "sysstuff.h"
+#include "gromacs/utility/cstringutil.h"
+#include "network.h"
+#include "gromacs/utility/smalloc.h"
+#include "nrnb.h"
+#include "main.h"
+#include "force.h"
+#include "macros.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "txtdump.h"
+#include "typedefs.h"
+#include "update.h"
+#include "constr.h"
+#include "vec.h"
+#include "tgroup.h"
+#include "mdebin.h"
+#include "vsite.h"
+#include "force.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "sim_util.h"
+#include "domdec.h"
+#include "mdatoms.h"
+#include "ns.h"
+#include "mtop_util.h"
+#include "pme.h"
+#include "bondf.h"
+#include "gmx_omp_nthreads.h"
+#include "md_logging.h"
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/imd/imd.h"
+
+typedef struct {
+    t_state  s;
+    rvec    *f;
+    real     epot;
+    real     fnorm;
+    real     fmax;
+    int      a_fmax;
+} em_state_t;
+
+static em_state_t *init_em_state()
+{
+    em_state_t *ems;
+
+    snew(ems, 1);
+
+    /* does this need to be here?  Should the array be declared differently (staticaly)in the state definition? */
+    snew(ems->s.lambda, efptNR);
+
+    return ems;
+}
+
+static void print_em_start(FILE                     *fplog,
+                           t_commrec                *cr,
+                           gmx_walltime_accounting_t walltime_accounting,
+                           gmx_wallcycle_t           wcycle,
+                           const char               *name)
+{
+    walltime_accounting_start(walltime_accounting);
+    wallcycle_start(wcycle, ewcRUN);
+    print_start(fplog, cr, walltime_accounting, name);
+}
+static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
+                        gmx_wallcycle_t           wcycle)
+{
+    wallcycle_stop(wcycle, ewcRUN);
+
+    walltime_accounting_end(walltime_accounting);
+}
+
+static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
+{
+    fprintf(out, "\n");
+    fprintf(out, "%s:\n", minimizer);
+    fprintf(out, "   Tolerance (Fmax)   = %12.5e\n", ftol);
+    fprintf(out, "   Number of steps    = %12d\n", nsteps);
+}
+
+static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
+{
+    char buffer[2048];
+    if (bLastStep)
+    {
+        sprintf(buffer,
+                "\nEnergy minimization reached the maximum number "
+                "of steps before the forces reached the requested "
+                "precision Fmax < %g.\n", ftol);
+    }
+    else
+    {
+        sprintf(buffer,
+                "\nEnergy minimization has stopped, but the forces have "
+                "not converged to the requested precision Fmax < %g (which "
+                "may not be possible for your system). It stopped "
+                "because the algorithm tried to make a new step whose size "
+                "was too small, or there was no change in the energy since "
+                "last step. Either way, we regard the minimization as "
+                "converged to within the available machine precision, "
+                "given your starting configuration and EM parameters.\n%s%s",
+                ftol,
+                sizeof(real) < sizeof(double) ?
+                "\nDouble precision normally gives you higher accuracy, but "
+                "this is often not needed for preparing to run molecular "
+                "dynamics.\n" :
+                "",
+                bConstrain ?
+                "You might need to increase your constraint accuracy, or turn\n"
+                "off constraints altogether (set constraints = none in mdp file)\n" :
+                "");
+    }
+    fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
+}
+
+
+
+static void print_converged(FILE *fp, const char *alg, real ftol,
+                            gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
+                            real epot, real fmax, int nfmax, real fnorm)
+{
+    char buf[STEPSTRSIZE];
+
+    if (bDone)
+    {
+        fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n",
+                alg, ftol, gmx_step_str(count, buf));
+    }
+    else if (count < nsteps)
+    {
+        fprintf(fp, "\n%s converged to machine precision in %s steps,\n"
+                "but did not reach the requested Fmax < %g.\n",
+                alg, gmx_step_str(count, buf), ftol);
+    }
+    else
+    {
+        fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n",
+                alg, ftol, gmx_step_str(count, buf));
+    }
+
+#ifdef GMX_DOUBLE
+    fprintf(fp, "Potential Energy  = %21.14e\n", epot);
+    fprintf(fp, "Maximum force     = %21.14e on atom %d\n", fmax, nfmax+1);
+    fprintf(fp, "Norm of force     = %21.14e\n", fnorm);
+#else
+    fprintf(fp, "Potential Energy  = %14.7e\n", epot);
+    fprintf(fp, "Maximum force     = %14.7e on atom %d\n", fmax, nfmax+1);
+    fprintf(fp, "Norm of force     = %14.7e\n", fnorm);
+#endif
+}
+
+static void get_f_norm_max(t_commrec *cr,
+                           t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
+                           real *fnorm, real *fmax, int *a_fmax)
+{
+    double fnorm2, *sum;
+    real   fmax2, fmax2_0, fam;
+    int    la_max, a_max, start, end, i, m, gf;
+
+    /* This routine finds the largest force and returns it.
+     * On parallel machines the global max is taken.
+     */
+    fnorm2 = 0;
+    fmax2  = 0;
+    la_max = -1;
+    gf     = 0;
+    start  = 0;
+    end    = mdatoms->homenr;
+    if (mdatoms->cFREEZE)
+    {
+        for (i = start; i < end; i++)
+        {
+            gf  = mdatoms->cFREEZE[i];
+            fam = 0;
+            for (m = 0; m < DIM; m++)
+            {
+                if (!opts->nFreeze[gf][m])
+                {
+                    fam += sqr(f[i][m]);
+                }
+            }
+            fnorm2 += fam;
+            if (fam > fmax2)
+            {
+                fmax2  = fam;
+                la_max = i;
+            }
+        }
+    }
+    else
+    {
+        for (i = start; i < end; i++)
+        {
+            fam     = norm2(f[i]);
+            fnorm2 += fam;
+            if (fam > fmax2)
+            {
+                fmax2  = fam;
+                la_max = i;
+            }
+        }
+    }
+
+    if (la_max >= 0 && DOMAINDECOMP(cr))
+    {
+        a_max = cr->dd->gatindex[la_max];
+    }
+    else
+    {
+        a_max = la_max;
+    }
+    if (PAR(cr))
+    {
+        snew(sum, 2*cr->nnodes+1);
+        sum[2*cr->nodeid]   = fmax2;
+        sum[2*cr->nodeid+1] = a_max;
+        sum[2*cr->nnodes]   = fnorm2;
+        gmx_sumd(2*cr->nnodes+1, sum, cr);
+        fnorm2 = sum[2*cr->nnodes];
+        /* Determine the global maximum */
+        for (i = 0; i < cr->nnodes; i++)
+        {
+            if (sum[2*i] > fmax2)
+            {
+                fmax2 = sum[2*i];
+                a_max = (int)(sum[2*i+1] + 0.5);
+            }
+        }
+        sfree(sum);
+    }
+
+    if (fnorm)
+    {
+        *fnorm = sqrt(fnorm2);
+    }
+    if (fmax)
+    {
+        *fmax  = sqrt(fmax2);
+    }
+    if (a_fmax)
+    {
+        *a_fmax = a_max;
+    }
+}
+
+static void get_state_f_norm_max(t_commrec *cr,
+                                 t_grpopts *opts, t_mdatoms *mdatoms,
+                                 em_state_t *ems)
+{
+    get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
+}
+
+void init_em(FILE *fplog, const char *title,
+             t_commrec *cr, t_inputrec *ir,
+             t_state *state_global, gmx_mtop_t *top_global,
+             em_state_t *ems, gmx_localtop_t **top,
+             rvec **f, rvec **f_global,
+             t_nrnb *nrnb, rvec mu_tot,
+             t_forcerec *fr, gmx_enerdata_t **enerd,
+             t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
+             gmx_vsite_t *vsite, gmx_constr_t constr,
+             int nfile, const t_filenm fnm[],
+             gmx_mdoutf_t *outf, t_mdebin **mdebin,
+             int imdport, unsigned long gmx_unused Flags,
+             gmx_wallcycle_t wcycle)
+{
+    int  i;
+    real dvdl_constr;
+
+    if (fplog)
+    {
+        fprintf(fplog, "Initiating %s\n", title);
+    }
+
+    state_global->ngtc = 0;
+
+    /* Initialize lambda variables */
+    initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, NULL);
+
+    init_nrnb(nrnb);
+
+    /* Interactive molecular dynamics */
+    init_IMD(ir, cr, top_global, fplog, 1, state_global->x,
+             nfile, fnm, NULL, imdport, Flags);
+
+    if (DOMAINDECOMP(cr))
+    {
+        *top = dd_init_local_top(top_global);
+
+        dd_init_local_state(cr->dd, state_global, &ems->s);
+
+        *f = NULL;
+
+        /* Distribute the charge groups over the nodes from the master node */
+        dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+                            state_global, top_global, ir,
+                            &ems->s, &ems->f, mdatoms, *top,
+                            fr, vsite, NULL, constr,
+                            nrnb, NULL, FALSE);
+        dd_store_state(cr->dd, &ems->s);
+
+        if (ir->nstfout)
+        {
+            snew(*f_global, top_global->natoms);
+        }
+        else
+        {
+            *f_global = NULL;
+        }
+        *graph = NULL;
+    }
+    else
+    {
+        snew(*f, top_global->natoms);
+
+        /* Just copy the state */
+        ems->s = *state_global;
+        snew(ems->s.x, ems->s.nalloc);
+        snew(ems->f, ems->s.nalloc);
+        for (i = 0; i < state_global->natoms; i++)
+        {
+            copy_rvec(state_global->x[i], ems->s.x[i]);
+        }
+        copy_mat(state_global->box, ems->s.box);
+
+        *top      = gmx_mtop_generate_local_top(top_global, ir);
+        *f_global = *f;
+
+        forcerec_set_excl_load(fr, *top);
+
+        setup_bonded_threading(fr, &(*top)->idef);
+
+        if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+        {
+            *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
+        }
+        else
+        {
+            *graph = NULL;
+        }
+
+        atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+        update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
+
+        if (vsite)
+        {
+            set_vsite_top(vsite, *top, mdatoms, cr);
+        }
+    }
+
+    if (constr)
+    {
+        if (ir->eConstrAlg == econtSHAKE &&
+            gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
+        {
+            gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
+                      econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+        }
+
+        if (!DOMAINDECOMP(cr))
+        {
+            set_constraints(constr, *top, ir, mdatoms, cr);
+        }
+
+        if (!ir->bContinuation)
+        {
+            /* Constrain the starting coordinates */
+            dvdl_constr = 0;
+            constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
+                      ir, NULL, cr, -1, 0, 1.0, mdatoms,
+                      ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
+                      ems->s.lambda[efptFEP], &dvdl_constr,
+                      NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+        }
+    }
+
+    if (PAR(cr))
+    {
+        *gstat = global_stat_init(ir);
+    }
+
+    *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
+
+    snew(*enerd, 1);
+    init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+                  *enerd);
+
+    if (mdebin != NULL)
+    {
+        /* Init bin for energy stuff */
+        *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, NULL);
+    }
+
+    clear_rvec(mu_tot);
+    calc_shifts(ems->s.box, fr->shift_vec);
+}
+
+static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
+                      gmx_walltime_accounting_t walltime_accounting,
+                      gmx_wallcycle_t wcycle)
+{
+    if (!(cr->duty & DUTY_PME))
+    {
+        /* Tell the PME only node to finish */
+        gmx_pme_send_finish(cr);
+    }
+
+    done_mdoutf(outf);
+
+    em_time_end(walltime_accounting, wcycle);
+}
+
+static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
+{
+    em_state_t tmp;
+
+    tmp   = *ems1;
+    *ems1 = *ems2;
+    *ems2 = tmp;
+}
+
+static void copy_em_coords(em_state_t *ems, t_state *state)
+{
+    int i;
+
+    for (i = 0; (i < state->natoms); i++)
+    {
+        copy_rvec(ems->s.x[i], state->x[i]);
+    }
+}
+
+static void write_em_traj(FILE *fplog, t_commrec *cr,
+                          gmx_mdoutf_t outf,
+                          gmx_bool bX, gmx_bool bF, const char *confout,
+                          gmx_mtop_t *top_global,
+                          t_inputrec *ir, gmx_int64_t step,
+                          em_state_t *state,
+                          t_state *state_global, rvec *f_global)
+{
+    int      mdof_flags;
+    gmx_bool bIMDout = FALSE;
+
+
+    /* Shall we do IMD output? */
+    if (ir->bIMD)
+    {
+        bIMDout = do_per_step(step, IMD_get_step(ir->imd->setup));
+    }
+
+    if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
+    {
+        copy_em_coords(state, state_global);
+        f_global = state->f;
+    }
+
+    mdof_flags = 0;
+    if (bX)
+    {
+        mdof_flags |= MDOF_X;
+    }
+    if (bF)
+    {
+        mdof_flags |= MDOF_F;
+    }
+
+    /* If we want IMD output, set appropriate MDOF flag */
+    if (ir->bIMD)
+    {
+        mdof_flags |= MDOF_IMD;
+    }
+
+    mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+                                     top_global, step, (double)step,
+                                     &state->s, state_global, state->f, f_global);
+
+    if (confout != NULL && MASTER(cr))
+    {
+        if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+        {
+            /* Make molecules whole only for confout writing */
+            do_pbc_mtop(fplog, ir->ePBC, state_global->box, top_global,
+                        state_global->x);
+        }
+
+        write_sto_conf_mtop(confout,
+                            *top_global->name, top_global,
+                            state_global->x, NULL, ir->ePBC, state_global->box);
+    }
+}
+
+static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
+                       gmx_bool bMolPBC,
+                       em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
+                       gmx_constr_t constr, gmx_localtop_t *top,
+                       t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+                       gmx_int64_t count)
+
+{
+    t_state *s1, *s2;
+    int      i;
+    int      start, end;
+    rvec    *x1, *x2;
+    real     dvdl_constr;
+    int      nthreads gmx_unused;
+
+    s1 = &ems1->s;
+    s2 = &ems2->s;
+
+    if (DOMAINDECOMP(cr) && s1->ddp_count != cr->dd->ddp_count)
+    {
+        gmx_incons("state mismatch in do_em_step");
+    }
+
+    s2->flags = s1->flags;
+
+    if (s2->nalloc != s1->nalloc)
+    {
+        s2->nalloc = s1->nalloc;
+        srenew(s2->x, s1->nalloc);
+        srenew(ems2->f,  s1->nalloc);
+        if (s2->flags & (1<<estCGP))
+        {
+            srenew(s2->cg_p,  s1->nalloc);
+        }
+    }
+
+    s2->natoms = s1->natoms;
+    copy_mat(s1->box, s2->box);
+    /* Copy free energy state */
+    for (i = 0; i < efptNR; i++)
+    {
+        s2->lambda[i] = s1->lambda[i];
+    }
+    copy_mat(s1->box, s2->box);
+
+    start = 0;
+    end   = md->homenr;
+
+    x1 = s1->x;
+    x2 = s2->x;
+
+    nthreads = gmx_omp_nthreads_get(emntUpdate);
+#pragma omp parallel num_threads(nthreads)
+    {
+        int gf, i, m;
+
+        gf = 0;
+#pragma omp for schedule(static) nowait
+        for (i = start; i < end; i++)
+        {
+            if (md->cFREEZE)
+            {
+                gf = md->cFREEZE[i];
+            }
+            for (m = 0; m < DIM; m++)
+            {
+                if (ir->opts.nFreeze[gf][m])
+                {
+                    x2[i][m] = x1[i][m];
+                }
+                else
+                {
+                    x2[i][m] = x1[i][m] + a*f[i][m];
+                }
+            }
+        }
+
+        if (s2->flags & (1<<estCGP))
+        {
+            /* Copy the CG p vector */
+            x1 = s1->cg_p;
+            x2 = s2->cg_p;
+#pragma omp for schedule(static) nowait
+            for (i = start; i < end; i++)
+            {
+                copy_rvec(x1[i], x2[i]);
+            }
+        }
+
+        if (DOMAINDECOMP(cr))
+        {
+            s2->ddp_count = s1->ddp_count;
+            if (s2->cg_gl_nalloc < s1->cg_gl_nalloc)
+            {
+#pragma omp barrier
+                s2->cg_gl_nalloc = s1->cg_gl_nalloc;
+                srenew(s2->cg_gl, s2->cg_gl_nalloc);
+#pragma omp barrier
+            }
+            s2->ncg_gl = s1->ncg_gl;
+#pragma omp for schedule(static) nowait
+            for (i = 0; i < s2->ncg_gl; i++)
+            {
+                s2->cg_gl[i] = s1->cg_gl[i];
+            }
+            s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
+        }
+    }
+
+    if (constr)
+    {
+        wallcycle_start(wcycle, ewcCONSTR);
+        dvdl_constr = 0;
+        constrain(NULL, TRUE, TRUE, constr, &top->idef,
+                  ir, NULL, cr, count, 0, 1.0, md,
+                  s1->x, s2->x, NULL, bMolPBC, s2->box,
+                  s2->lambda[efptBONDED], &dvdl_constr,
+                  NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+        wallcycle_stop(wcycle, ewcCONSTR);
+    }
+}
+
+static void em_dd_partition_system(FILE *fplog, int step, t_commrec *cr,
+                                   gmx_mtop_t *top_global, t_inputrec *ir,
+                                   em_state_t *ems, gmx_localtop_t *top,
+                                   t_mdatoms *mdatoms, t_forcerec *fr,
+                                   gmx_vsite_t *vsite, gmx_constr_t constr,
+                                   t_nrnb *nrnb, gmx_wallcycle_t wcycle)
+{
+    /* Repartition the domain decomposition */
+    wallcycle_start(wcycle, ewcDOMDEC);
+    dd_partition_system(fplog, step, cr, FALSE, 1,
+                        NULL, top_global, ir,
+                        &ems->s, &ems->f,
+                        mdatoms, top, fr, vsite, NULL, constr,
+                        nrnb, wcycle, FALSE);
+    dd_store_state(cr->dd, &ems->s);
+    wallcycle_stop(wcycle, ewcDOMDEC);
+}
+
+static void evaluate_energy(FILE *fplog, t_commrec *cr,
+                            gmx_mtop_t *top_global,
+                            em_state_t *ems, gmx_localtop_t *top,
+                            t_inputrec *inputrec,
+                            t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+                            gmx_global_stat_t gstat,
+                            gmx_vsite_t *vsite, gmx_constr_t constr,
+                            t_fcdata *fcd,
+                            t_graph *graph, t_mdatoms *mdatoms,
+                            t_forcerec *fr, rvec mu_tot,
+                            gmx_enerdata_t *enerd, tensor vir, tensor pres,
+                            gmx_int64_t count, gmx_bool bFirst)
+{
+    real     t;
+    gmx_bool bNS;
+    int      nabnsb;
+    tensor   force_vir, shake_vir, ekin;
+    real     dvdl_constr, prescorr, enercorr, dvdlcorr;
+    real     terminate = 0;
+
+    /* Set the time to the initial time, the time does not change during EM */
+    t = inputrec->init_t;
+
+    if (bFirst ||
+        (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
+    {
+        /* This is the first state or an old state used before the last ns */
+        bNS = TRUE;
+    }
+    else
+    {
+        bNS = FALSE;
+        if (inputrec->nstlist > 0)
+        {
+            bNS = TRUE;
+        }
+        else if (inputrec->nstlist == -1)
+        {
+            nabnsb = natoms_beyond_ns_buffer(inputrec, fr, &top->cgs, NULL, ems->s.x);
+            if (PAR(cr))
+            {
+                gmx_sumi(1, &nabnsb, cr);
+            }
+            bNS = (nabnsb > 0);
+        }
+    }
+
+    if (vsite)
+    {
+        construct_vsites(vsite, ems->s.x, 1, NULL,
+                         top->idef.iparams, top->idef.il,
+                         fr->ePBC, fr->bMolPBC, cr, ems->s.box);
+    }
+
+    if (DOMAINDECOMP(cr) && bNS)
+    {
+        /* Repartition the domain decomposition */
+        em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+                               ems, top, mdatoms, fr, vsite, constr,
+                               nrnb, wcycle);
+    }
+
+    /* Calc force & energy on new trial position  */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole in congrad.c
+     */
+    do_force(fplog, cr, inputrec,
+             count, nrnb, wcycle, top, &top_global->groups,
+             ems->s.box, ems->s.x, &ems->s.hist,
+             ems->f, force_vir, mdatoms, enerd, fcd,
+             ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
+             GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
+             GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
+             (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
+
+    /* Clear the unused shake virial and pressure */
+    clear_mat(shake_vir);
+    clear_mat(pres);
+
+    /* Communicate stuff when parallel */
+    if (PAR(cr) && inputrec->eI != eiNM)
+    {
+        wallcycle_start(wcycle, ewcMoveE);
+
+        global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
+                    inputrec, NULL, NULL, NULL, 1, &terminate,
+                    top_global, &ems->s, FALSE,
+                    CGLO_ENERGY |
+                    CGLO_PRESSURE |
+                    CGLO_CONSTRAINT |
+                    CGLO_FIRSTITERATE);
+
+        wallcycle_stop(wcycle, ewcMoveE);
+    }
+
+    /* Calculate long range corrections to pressure and energy */
+    calc_dispcorr(fplog, inputrec, fr, count, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
+                  pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
+    enerd->term[F_DISPCORR] = enercorr;
+    enerd->term[F_EPOT]    += enercorr;
+    enerd->term[F_PRES]    += prescorr;
+    enerd->term[F_DVDL]    += dvdlcorr;
+
+    ems->epot = enerd->term[F_EPOT];
+
+    if (constr)
+    {
+        /* Project out the constraint components of the force */
+        wallcycle_start(wcycle, ewcCONSTR);
+        dvdl_constr = 0;
+        constrain(NULL, FALSE, FALSE, constr, &top->idef,
+                  inputrec, NULL, cr, count, 0, 1.0, mdatoms,
+                  ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
+                  ems->s.lambda[efptBONDED], &dvdl_constr,
+                  NULL, &shake_vir, nrnb, econqForceDispl, FALSE, 0, 0);
+        if (fr->bSepDVDL && fplog)
+        {
+            gmx_print_sepdvdl(fplog, "Constraints", t, dvdl_constr);
+        }
+        enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+        m_add(force_vir, shake_vir, vir);
+        wallcycle_stop(wcycle, ewcCONSTR);
+    }
+    else
+    {
+        copy_mat(force_vir, vir);
+    }
+
+    clear_mat(ekin);
+    enerd->term[F_PRES] =
+        calc_pres(fr->ePBC, inputrec->nwall, ems->s.box, ekin, vir, pres);
+
+    sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
+
+    if (EI_ENERGY_MINIMIZATION(inputrec->eI))
+    {
+        get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, ems);
+    }
+}
+
+static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+                              gmx_mtop_t *mtop,
+                              em_state_t *s_min, em_state_t *s_b)
+{
+    rvec          *fm, *fb, *fmg;
+    t_block       *cgs_gl;
+    int            ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
+    double         partsum;
+    unsigned char *grpnrFREEZE;
+
+    if (debug)
+    {
+        fprintf(debug, "Doing reorder_partsum\n");
+    }
+
+    fm = s_min->f;
+    fb = s_b->f;
+
+    cgs_gl = dd_charge_groups_global(cr->dd);
+    index  = cgs_gl->index;
+
+    /* Collect fm in a global vector fmg.
+     * This conflicts with the spirit of domain decomposition,
+     * but to fully optimize this a much more complicated algorithm is required.
+     */
+    snew(fmg, mtop->natoms);
+
+    ncg   = s_min->s.ncg_gl;
+    cg_gl = s_min->s.cg_gl;
+    i     = 0;
+    for (c = 0; c < ncg; c++)
+    {
+        cg = cg_gl[c];
+        a0 = index[cg];
+        a1 = index[cg+1];
+        for (a = a0; a < a1; a++)
+        {
+            copy_rvec(fm[i], fmg[a]);
+            i++;
+        }
+    }
+    gmx_sum(mtop->natoms*3, fmg[0], cr);
+
+    /* Now we will determine the part of the sum for the cgs in state s_b */
+    ncg         = s_b->s.ncg_gl;
+    cg_gl       = s_b->s.cg_gl;
+    partsum     = 0;
+    i           = 0;
+    gf          = 0;
+    grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
+    for (c = 0; c < ncg; c++)
+    {
+        cg = cg_gl[c];
+        a0 = index[cg];
+        a1 = index[cg+1];
+        for (a = a0; a < a1; a++)
+        {
+            if (mdatoms->cFREEZE && grpnrFREEZE)
+            {
+                gf = grpnrFREEZE[i];
+            }
+            for (m = 0; m < DIM; m++)
+            {
+                if (!opts->nFreeze[gf][m])
+                {
+                    partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
+                }
+            }
+            i++;
+        }
+    }
+
+    sfree(fmg);
+
+    return partsum;
+}
+
+static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+                    gmx_mtop_t *mtop,
+                    em_state_t *s_min, em_state_t *s_b)
+{
+    rvec  *fm, *fb;
+    double sum;
+    int    gf, i, m;
+
+    /* This is just the classical Polak-Ribiere calculation of beta;
+     * it looks a bit complicated since we take freeze groups into account,
+     * and might have to sum it in parallel runs.
+     */
+
+    if (!DOMAINDECOMP(cr) ||
+        (s_min->s.ddp_count == cr->dd->ddp_count &&
+         s_b->s.ddp_count   == cr->dd->ddp_count))
+    {
+        fm  = s_min->f;
+        fb  = s_b->f;
+        sum = 0;
+        gf  = 0;
+        /* This part of code can be incorrect with DD,
+         * since the atom ordering in s_b and s_min might differ.
+         */
+        for (i = 0; i < mdatoms->homenr; i++)
+        {
+            if (mdatoms->cFREEZE)
+            {
+                gf = mdatoms->cFREEZE[i];
+            }
+            for (m = 0; m < DIM; m++)
+            {
+                if (!opts->nFreeze[gf][m])
+                {
+                    sum += (fb[i][m] - fm[i][m])*fb[i][m];
+                }
+            }
+        }
+    }
+    else
+    {
+        /* We need to reorder cgs while summing */
+        sum = reorder_partsum(cr, opts, mdatoms, mtop, s_min, s_b);
+    }
+    if (PAR(cr))
+    {
+        gmx_sumd(1, &sum, cr);
+    }
+
+    return sum/sqr(s_min->fnorm);
+}
+
+double do_cg(FILE *fplog, t_commrec *cr,
+             int nfile, const t_filenm fnm[],
+             const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+             int gmx_unused nstglobalcomm,
+             gmx_vsite_t *vsite, gmx_constr_t constr,
+             int gmx_unused stepout,
+             t_inputrec *inputrec,
+             gmx_mtop_t *top_global, t_fcdata *fcd,
+             t_state *state_global,
+             t_mdatoms *mdatoms,
+             t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+             gmx_edsam_t gmx_unused ed,
+             t_forcerec *fr,
+             int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+             gmx_membed_t gmx_unused membed,
+             real gmx_unused cpt_period, real gmx_unused max_hours,
+             const char gmx_unused *deviceOptions,
+             int imdport,
+             unsigned long gmx_unused Flags,
+             gmx_walltime_accounting_t walltime_accounting)
+{
+    const char       *CG = "Polak-Ribiere Conjugate Gradients";
+
+    em_state_t       *s_min, *s_a, *s_b, *s_c;
+    gmx_localtop_t   *top;
+    gmx_enerdata_t   *enerd;
+    rvec             *f;
+    gmx_global_stat_t gstat;
+    t_graph          *graph;
+    rvec             *f_global, *p, *sf, *sfm;
+    double            gpa, gpb, gpc, tmp, sum[2], minstep;
+    real              fnormn;
+    real              stepsize;
+    real              a, b, c, beta = 0.0;
+    real              epot_repl = 0;
+    real              pnorm;
+    t_mdebin         *mdebin;
+    gmx_bool          converged, foundlower;
+    rvec              mu_tot;
+    gmx_bool          do_log = FALSE, do_ene = FALSE, do_x, do_f;
+    tensor            vir, pres;
+    int               number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
+    gmx_mdoutf_t      outf;
+    int               i, m, gf, step, nminstep;
+    real              terminate = 0;
+
+    step = 0;
+
+    s_min = init_em_state();
+    s_a   = init_em_state();
+    s_b   = init_em_state();
+    s_c   = init_em_state();
+
+    /* Init em and store the local state in s_min */
+    init_em(fplog, CG, cr, inputrec,
+            state_global, top_global, s_min, &top, &f, &f_global,
+            nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+
+    /* Print to log file */
+    print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
+
+    /* Max number of steps */
+    number_steps = inputrec->nsteps;
+
+    if (MASTER(cr))
+    {
+        sp_header(stderr, CG, inputrec->em_tol, number_steps);
+    }
+    if (fplog)
+    {
+        sp_header(fplog, CG, inputrec->em_tol, number_steps);
+    }
+
+    /* Call the force routine and some auxiliary (neighboursearching etc.) */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole in congrad.c
+     */
+    evaluate_energy(fplog, cr,
+                    top_global, s_min, top,
+                    inputrec, nrnb, wcycle, gstat,
+                    vsite, constr, fcd, graph, mdatoms, fr,
+                    mu_tot, enerd, vir, pres, -1, TRUE);
+    where();
+
+    if (MASTER(cr))
+    {
+        /* Copy stuff to the energy bin for easy printing etc. */
+        upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+                   mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+                   NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+        print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+        print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+                   TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+    }
+    where();
+
+    /* Estimate/guess the initial stepsize */
+    stepsize = inputrec->em_stepsize/s_min->fnorm;
+
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "   F-max             = %12.5e on atom %d\n",
+                s_min->fmax, s_min->a_fmax+1);
+        fprintf(stderr, "   F-Norm            = %12.5e\n",
+                s_min->fnorm/sqrt(state_global->natoms));
+        fprintf(stderr, "\n");
+        /* and copy to the log file too... */
+        fprintf(fplog, "   F-max             = %12.5e on atom %d\n",
+                s_min->fmax, s_min->a_fmax+1);
+        fprintf(fplog, "   F-Norm            = %12.5e\n",
+                s_min->fnorm/sqrt(state_global->natoms));
+        fprintf(fplog, "\n");
+    }
+    /* Start the loop over CG steps.
+     * Each successful step is counted, and we continue until
+     * we either converge or reach the max number of steps.
+     */
+    converged = FALSE;
+    for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+    {
+
+        /* start taking steps in a new direction
+         * First time we enter the routine, beta=0, and the direction is
+         * simply the negative gradient.
+         */
+
+        /* Calculate the new direction in p, and the gradient in this direction, gpa */
+        p   = s_min->s.cg_p;
+        sf  = s_min->f;
+        gpa = 0;
+        gf  = 0;
+        for (i = 0; i < mdatoms->homenr; i++)
+        {
+            if (mdatoms->cFREEZE)
+            {
+                gf = mdatoms->cFREEZE[i];
+            }
+            for (m = 0; m < DIM; m++)
+            {
+                if (!inputrec->opts.nFreeze[gf][m])
+                {
+                    p[i][m] = sf[i][m] + beta*p[i][m];
+                    gpa    -= p[i][m]*sf[i][m];
+                    /* f is negative gradient, thus the sign */
+                }
+                else
+                {
+                    p[i][m] = 0;
+                }
+            }
+        }
+
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr))
+        {
+            gmx_sumd(1, &gpa, cr);
+        }
+
+        /* Calculate the norm of the search vector */
+        get_f_norm_max(cr, &(inputrec->opts), mdatoms, p, &pnorm, NULL, NULL);
+
+        /* Just in case stepsize reaches zero due to numerical precision... */
+        if (stepsize <= 0)
+        {
+            stepsize = inputrec->em_stepsize/pnorm;
+        }
+
+        /*
+         * Double check the value of the derivative in the search direction.
+         * If it is positive it must be due to the old information in the
+         * CG formula, so just remove that and start over with beta=0.
+         * This corresponds to a steepest descent step.
+         */
+        if (gpa > 0)
+        {
+            beta = 0;
+            step--;   /* Don't count this step since we are restarting */
+            continue; /* Go back to the beginning of the big for-loop */
+        }
+
+        /* Calculate minimum allowed stepsize, before the average (norm)
+         * relative change in coordinate is smaller than precision
+         */
+        minstep = 0;
+        for (i = 0; i < mdatoms->homenr; i++)
+        {
+            for (m = 0; m < DIM; m++)
+            {
+                tmp = fabs(s_min->s.x[i][m]);
+                if (tmp < 1.0)
+                {
+                    tmp = 1.0;
+                }
+                tmp      = p[i][m]/tmp;
+                minstep += tmp*tmp;
+            }
+        }
+        /* Add up from all CPUs */
+        if (PAR(cr))
+        {
+            gmx_sumd(1, &minstep, cr);
+        }
+
+        minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
+
+        if (stepsize < minstep)
+        {
+            converged = TRUE;
+            break;
+        }
+
+        /* Write coordinates if necessary */
+        do_x = do_per_step(step, inputrec->nstxout);
+        do_f = do_per_step(step, inputrec->nstfout);
+
+        write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+                      top_global, inputrec, step,
+                      s_min, state_global, f_global);
+
+        /* Take a step downhill.
+         * In theory, we should minimize the function along this direction.
+         * That is quite possible, but it turns out to take 5-10 function evaluations
+         * for each line. However, we dont really need to find the exact minimum -
+         * it is much better to start a new CG step in a modified direction as soon
+         * as we are close to it. This will save a lot of energy evaluations.
+         *
+         * In practice, we just try to take a single step.
+         * If it worked (i.e. lowered the energy), we increase the stepsize but
+         * the continue straight to the next CG step without trying to find any minimum.
+         * If it didn't work (higher energy), there must be a minimum somewhere between
+         * the old position and the new one.
+         *
+         * Due to the finite numerical accuracy, it turns out that it is a good idea
+         * to even accept a SMALL increase in energy, if the derivative is still downhill.
+         * This leads to lower final energies in the tests I've done. / Erik
+         */
+        s_a->epot = s_min->epot;
+        a         = 0.0;
+        c         = a + stepsize; /* reference position along line is zero */
+
+        if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
+        {
+            em_dd_partition_system(fplog, step, cr, top_global, inputrec,
+                                   s_min, top, mdatoms, fr, vsite, constr,
+                                   nrnb, wcycle);
+        }
+
+        /* Take a trial step (new coords in s_c) */
+        do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, s_min->s.cg_p, s_c,
+                   constr, top, nrnb, wcycle, -1);
+
+        neval++;
+        /* Calculate energy for the trial step */
+        evaluate_energy(fplog, cr,
+                        top_global, s_c, top,
+                        inputrec, nrnb, wcycle, gstat,
+                        vsite, constr, fcd, graph, mdatoms, fr,
+                        mu_tot, enerd, vir, pres, -1, FALSE);
+
+        /* Calc derivative along line */
+        p   = s_c->s.cg_p;
+        sf  = s_c->f;
+        gpc = 0;
+        for (i = 0; i < mdatoms->homenr; i++)
+        {
+            for (m = 0; m < DIM; m++)
+            {
+                gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+            }
+        }
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr))
+        {
+            gmx_sumd(1, &gpc, cr);
+        }
+
+        /* This is the max amount of increase in energy we tolerate */
+        tmp = sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
+
+        /* Accept the step if the energy is lower, or if it is not significantly higher
+         * and the line derivative is still negative.
+         */
+        if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
+        {
+            foundlower = TRUE;
+            /* Great, we found a better energy. Increase step for next iteration
+             * if we are still going down, decrease it otherwise
+             */
+            if (gpc < 0)
+            {
+                stepsize *= 1.618034; /* The golden section */
+            }
+            else
+            {
+                stepsize *= 0.618034; /* 1/golden section */
+            }
+        }
+        else
+        {
+            /* New energy is the same or higher. We will have to do some work
+             * to find a smaller value in the interval. Take smaller step next time!
+             */
+            foundlower = FALSE;
+            stepsize  *= 0.618034;
+        }
+
+
+
+
+        /* OK, if we didn't find a lower value we will have to locate one now - there must
+         * be one in the interval [a=0,c].
+         * The same thing is valid here, though: Don't spend dozens of iterations to find
+         * the line minimum. We try to interpolate based on the derivative at the endpoints,
+         * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+         *
+         * I also have a safeguard for potentially really patological functions so we never
+         * take more than 20 steps before we give up ...
+         *
+         * If we already found a lower value we just skip this step and continue to the update.
+         */
+        if (!foundlower)
+        {
+            nminstep = 0;
+
+            do
+            {
+                /* Select a new trial point.
+                 * If the derivatives at points a & c have different sign we interpolate to zero,
+                 * otherwise just do a bisection.
+                 */
+                if (gpa < 0 && gpc > 0)
+                {
+                    b = a + gpa*(a-c)/(gpc-gpa);
+                }
+                else
+                {
+                    b = 0.5*(a+c);
+                }
+
+                /* safeguard if interpolation close to machine accuracy causes errors:
+                 * never go outside the interval
+                 */
+                if (b <= a || b >= c)
+                {
+                    b = 0.5*(a+c);
+                }
+
+                if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+                {
+                    /* Reload the old state */
+                    em_dd_partition_system(fplog, -1, cr, top_global, inputrec,
+                                           s_min, top, mdatoms, fr, vsite, constr,
+                                           nrnb, wcycle);
+                }
+
+                /* Take a trial step to this new point - new coords in s_b */
+                do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, s_min->s.cg_p, s_b,
+                           constr, top, nrnb, wcycle, -1);
+
+                neval++;
+                /* Calculate energy for the trial step */
+                evaluate_energy(fplog, cr,
+                                top_global, s_b, top,
+                                inputrec, nrnb, wcycle, gstat,
+                                vsite, constr, fcd, graph, mdatoms, fr,
+                                mu_tot, enerd, vir, pres, -1, FALSE);
+
+                /* p does not change within a step, but since the domain decomposition
+                 * might change, we have to use cg_p of s_b here.
+                 */
+                p   = s_b->s.cg_p;
+                sf  = s_b->f;
+                gpb = 0;
+                for (i = 0; i < mdatoms->homenr; i++)
+                {
+                    for (m = 0; m < DIM; m++)
+                    {
+                        gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+                    }
+                }
+                /* Sum the gradient along the line across CPUs */
+                if (PAR(cr))
+                {
+                    gmx_sumd(1, &gpb, cr);
+                }
+
+                if (debug)
+                {
+                    fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
+                            s_a->epot, s_b->epot, s_c->epot, gpb);
+                }
+
+                epot_repl = s_b->epot;
+
+                /* Keep one of the intervals based on the value of the derivative at the new point */
+                if (gpb > 0)
+                {
+                    /* Replace c endpoint with b */
+                    swap_em_state(s_b, s_c);
+                    c   = b;
+                    gpc = gpb;
+                }
+                else
+                {
+                    /* Replace a endpoint with b */
+                    swap_em_state(s_b, s_a);
+                    a   = b;
+                    gpa = gpb;
+                }
+
+                /*
+                 * Stop search as soon as we find a value smaller than the endpoints.
+                 * Never run more than 20 steps, no matter what.
+                 */
+                nminstep++;
+            }
+            while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
+                   (nminstep < 20));
+
+            if (fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
+                nminstep >= 20)
+            {
+                /* OK. We couldn't find a significantly lower energy.
+                 * If beta==0 this was steepest descent, and then we give up.
+                 * If not, set beta=0 and restart with steepest descent before quitting.
+                 */
+                if (beta == 0.0)
+                {
+                    /* Converged */
+                    converged = TRUE;
+                    break;
+                }
+                else
+                {
+                    /* Reset memory before giving up */
+                    beta = 0.0;
+                    continue;
+                }
+            }
+
+            /* Select min energy state of A & C, put the best in B.
+             */
+            if (s_c->epot < s_a->epot)
+            {
+                if (debug)
+                {
+                    fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
+                            s_c->epot, s_a->epot);
+                }
+                swap_em_state(s_b, s_c);
+                gpb = gpc;
+                b   = c;
+            }
+            else
+            {
+                if (debug)
+                {
+                    fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
+                            s_a->epot, s_c->epot);
+                }
+                swap_em_state(s_b, s_a);
+                gpb = gpa;
+                b   = a;
+            }
+
+        }
+        else
+        {
+            if (debug)
+            {
+                fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
+                        s_c->epot);
+            }
+            swap_em_state(s_b, s_c);
+            gpb = gpc;
+            b   = c;
+        }
+
+        /* new search direction */
+        /* beta = 0 means forget all memory and restart with steepest descents. */
+        if (nstcg && ((step % nstcg) == 0))
+        {
+            beta = 0.0;
+        }
+        else
+        {
+            /* s_min->fnorm cannot be zero, because then we would have converged
+             * and broken out.
+             */
+
+            /* Polak-Ribiere update.
+             * Change to fnorm2/fnorm2_old for Fletcher-Reeves
+             */
+            beta = pr_beta(cr, &inputrec->opts, mdatoms, top_global, s_min, s_b);
+        }
+        /* Limit beta to prevent oscillations */
+        if (fabs(beta) > 5.0)
+        {
+            beta = 0.0;
+        }
+
+
+        /* update positions */
+        swap_em_state(s_min, s_b);
+        gpa = gpb;
+
+        /* Print it if necessary */
+        if (MASTER(cr))
+        {
+            if (bVerbose)
+            {
+                fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+                        step, s_min->epot, s_min->fnorm/sqrt(state_global->natoms),
+                        s_min->fmax, s_min->a_fmax+1);
+            }
+            /* Store the new (lower) energies */
+            upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+                       mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+                       NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+            do_log = do_per_step(step, inputrec->nstlog);
+            do_ene = do_per_step(step, inputrec->nstenergy);
+
+            /* Prepare IMD energy record, if bIMD is TRUE. */
+            IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
+
+            if (do_log)
+            {
+                print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+            }
+            print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+                       do_log ? fplog : NULL, step, step, eprNORMAL,
+                       TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+        }
+
+        /* Send energies and positions to the IMD client if bIMD is TRUE. */
+        if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+        {
+            IMD_send_positions(inputrec->imd);
+        }
+
+        /* Stop when the maximum force lies below tolerance.
+         * If we have reached machine precision, converged is already set to true.
+         */
+        converged = converged || (s_min->fmax < inputrec->em_tol);
+
+    } /* End of the loop */
+
+    /* IMD cleanup, if bIMD is TRUE. */
+    IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+    if (converged)
+    {
+        step--; /* we never took that last step in this case */
+
+    }
+    if (s_min->fmax > inputrec->em_tol)
+    {
+        if (MASTER(cr))
+        {
+            warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
+            warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
+        }
+        converged = FALSE;
+    }
+
+    if (MASTER(cr))
+    {
+        /* If we printed energy and/or logfile last step (which was the last step)
+         * we don't have to do it again, but otherwise print the final values.
+         */
+        if (!do_log)
+        {
+            /* Write final value to log since we didn't do anything the last step */
+            print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+        }
+        if (!do_ene || !do_log)
+        {
+            /* Write final energy file entries */
+            print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+                       !do_log ? fplog : NULL, step, step, eprNORMAL,
+                       TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+        }
+    }
+
+    /* Print some stuff... */
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+
+    /* IMPORTANT!
+     * For accurate normal mode calculation it is imperative that we
+     * store the last conformation into the full precision binary trajectory.
+     *
+     * However, we should only do it if we did NOT already write this step
+     * above (which we did if do_x or do_f was true).
+     */
+    do_x = !do_per_step(step, inputrec->nstxout);
+    do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
+
+    write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+                  top_global, inputrec, step,
+                  s_min, state_global, f_global);
+
+    fnormn = s_min->fnorm/sqrt(state_global->natoms);
+
+    if (MASTER(cr))
+    {
+        print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
+                        s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+        print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
+                        s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+
+        fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+    }
+
+    finish_em(cr, outf, walltime_accounting, wcycle);
+
+    /* To print the actual number of steps we needed somewhere */
+    walltime_accounting_set_nsteps_done(walltime_accounting, step);
+
+    return 0;
+} /* That's all folks */
+
+
+double do_lbfgs(FILE *fplog, t_commrec *cr,
+                int nfile, const t_filenm fnm[],
+                const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+                int gmx_unused nstglobalcomm,
+                gmx_vsite_t *vsite, gmx_constr_t constr,
+                int gmx_unused stepout,
+                t_inputrec *inputrec,
+                gmx_mtop_t *top_global, t_fcdata *fcd,
+                t_state *state,
+                t_mdatoms *mdatoms,
+                t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+                gmx_edsam_t gmx_unused ed,
+                t_forcerec *fr,
+                int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+                gmx_membed_t gmx_unused membed,
+                real gmx_unused cpt_period, real gmx_unused max_hours,
+                const char gmx_unused *deviceOptions,
+                int imdport,
+                unsigned long gmx_unused Flags,
+                gmx_walltime_accounting_t walltime_accounting)
+{
+    static const char *LBFGS = "Low-Memory BFGS Minimizer";
+    em_state_t         ems;
+    gmx_localtop_t    *top;
+    gmx_enerdata_t    *enerd;
+    rvec              *f;
+    gmx_global_stat_t  gstat;
+    t_graph           *graph;
+    rvec              *f_global;
+    int                ncorr, nmaxcorr, point, cp, neval, nminstep;
+    double             stepsize, gpa, gpb, gpc, tmp, minstep;
+    real              *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
+    real              *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
+    real               a, b, c, maxdelta, delta;
+    real               diag, Epot0, Epot, EpotA, EpotB, EpotC;
+    real               dgdx, dgdg, sq, yr, beta;
+    t_mdebin          *mdebin;
+    gmx_bool           converged, first;
+    rvec               mu_tot;
+    real               fnorm, fmax;
+    gmx_bool           do_log, do_ene, do_x, do_f, foundlower, *frozen;
+    tensor             vir, pres;
+    int                start, end, number_steps;
+    gmx_mdoutf_t       outf;
+    int                i, k, m, n, nfmax, gf, step;
+    int                mdof_flags;
+    /* not used */
+    real               terminate;
+
+    if (PAR(cr))
+    {
+        gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
+    }
+
+    if (NULL != constr)
+    {
+        gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
+    }
+
+    n        = 3*state->natoms;
+    nmaxcorr = inputrec->nbfgscorr;
+
+    /* Allocate memory */
+    /* Use pointers to real so we dont have to loop over both atoms and
+     * dimensions all the time...
+     * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
+     * that point to the same memory.
+     */
+    snew(xa, n);
+    snew(xb, n);
+    snew(xc, n);
+    snew(fa, n);
+    snew(fb, n);
+    snew(fc, n);
+    snew(frozen, n);
+
+    snew(p, n);
+    snew(lastx, n);
+    snew(lastf, n);
+    snew(rho, nmaxcorr);
+    snew(alpha, nmaxcorr);
+
+    snew(dx, nmaxcorr);
+    for (i = 0; i < nmaxcorr; i++)
+    {
+        snew(dx[i], n);
+    }
+
+    snew(dg, nmaxcorr);
+    for (i = 0; i < nmaxcorr; i++)
+    {
+        snew(dg[i], n);
+    }
+
+    step  = 0;
+    neval = 0;
+
+    /* Init em */
+    init_em(fplog, LBFGS, cr, inputrec,
+            state, top_global, &ems, &top, &f, &f_global,
+            nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+    /* Do_lbfgs is not completely updated like do_steep and do_cg,
+     * so we free some memory again.
+     */
+    sfree(ems.s.x);
+    sfree(ems.f);
+
+    xx = (real *)state->x;
+    ff = (real *)f;
+
+    start = 0;
+    end   = mdatoms->homenr;
+
+    /* Print to log file */
+    print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
+
+    do_log = do_ene = do_x = do_f = TRUE;
+
+    /* Max number of steps */
+    number_steps = inputrec->nsteps;
+
+    /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
+    gf = 0;
+    for (i = start; i < end; i++)
+    {
+        if (mdatoms->cFREEZE)
+        {
+            gf = mdatoms->cFREEZE[i];
+        }
+        for (m = 0; m < DIM; m++)
+        {
+            frozen[3*i+m] = inputrec->opts.nFreeze[gf][m];
+        }
+    }
+    if (MASTER(cr))
+    {
+        sp_header(stderr, LBFGS, inputrec->em_tol, number_steps);
+    }
+    if (fplog)
+    {
+        sp_header(fplog, LBFGS, inputrec->em_tol, number_steps);
+    }
+
+    if (vsite)
+    {
+        construct_vsites(vsite, state->x, 1, NULL,
+                         top->idef.iparams, top->idef.il,
+                         fr->ePBC, fr->bMolPBC, cr, state->box);
+    }
+
+    /* Call the force routine and some auxiliary (neighboursearching etc.) */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole
+     */
+    neval++;
+    ems.s.x = state->x;
+    ems.f   = f;
+    evaluate_energy(fplog, cr,
+                    top_global, &ems, top,
+                    inputrec, nrnb, wcycle, gstat,
+                    vsite, constr, fcd, graph, mdatoms, fr,
+                    mu_tot, enerd, vir, pres, -1, TRUE);
+    where();
+
+    if (MASTER(cr))
+    {
+        /* Copy stuff to the energy bin for easy printing etc. */
+        upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+                   mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+                   NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+        print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+        print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+                   TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+    }
+    where();
+
+    /* This is the starting energy */
+    Epot = enerd->term[F_EPOT];
+
+    fnorm = ems.fnorm;
+    fmax  = ems.fmax;
+    nfmax = ems.a_fmax;
+
+    /* Set the initial step.
+     * since it will be multiplied by the non-normalized search direction
+     * vector (force vector the first time), we scale it by the
+     * norm of the force.
+     */
+
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+        fprintf(stderr, "   F-max             = %12.5e on atom %d\n", fmax, nfmax+1);
+        fprintf(stderr, "   F-Norm            = %12.5e\n", fnorm/sqrt(state->natoms));
+        fprintf(stderr, "\n");
+        /* and copy to the log file too... */
+        fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+        fprintf(fplog, "   F-max             = %12.5e on atom %d\n", fmax, nfmax+1);
+        fprintf(fplog, "   F-Norm            = %12.5e\n", fnorm/sqrt(state->natoms));
+        fprintf(fplog, "\n");
+    }
+
+    point = 0;
+    for (i = 0; i < n; i++)
+    {
+        if (!frozen[i])
+        {
+            dx[point][i] = ff[i]; /* Initial search direction */
+        }
+        else
+        {
+            dx[point][i] = 0;
+        }
+    }
+
+    stepsize  = 1.0/fnorm;
+    converged = FALSE;
+
+    /* Start the loop over BFGS steps.
+     * Each successful step is counted, and we continue until
+     * we either converge or reach the max number of steps.
+     */
+
+    ncorr = 0;
+
+    /* Set the gradient from the force */
+    converged = FALSE;
+    for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+    {
+
+        /* Write coordinates if necessary */
+        do_x = do_per_step(step, inputrec->nstxout);
+        do_f = do_per_step(step, inputrec->nstfout);
+
+        mdof_flags = 0;
+        if (do_x)
+        {
+            mdof_flags |= MDOF_X;
+        }
+
+        if (do_f)
+        {
+            mdof_flags |= MDOF_F;
+        }
+
+        if (inputrec->bIMD)
+        {
+            mdof_flags |= MDOF_IMD;
+        }
+
+        mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+                                         top_global, step, (real)step, state, state, f, f);
+
+        /* Do the linesearching in the direction dx[point][0..(n-1)] */
+
+        /* pointer to current direction - point=0 first time here */
+        s = dx[point];
+
+        /* calculate line gradient */
+        for (gpa = 0, i = 0; i < n; i++)
+        {
+            gpa -= s[i]*ff[i];
+        }
+
+        /* Calculate minimum allowed stepsize, before the average (norm)
+         * relative change in coordinate is smaller than precision
+         */
+        for (minstep = 0, i = 0; i < n; i++)
+        {
+            tmp = fabs(xx[i]);
+            if (tmp < 1.0)
+            {
+                tmp = 1.0;
+            }
+            tmp      = s[i]/tmp;
+            minstep += tmp*tmp;
+        }
+        minstep = GMX_REAL_EPS/sqrt(minstep/n);
+
+        if (stepsize < minstep)
+        {
+            converged = TRUE;
+            break;
+        }
+
+        /* Store old forces and coordinates */
+        for (i = 0; i < n; i++)
+        {
+            lastx[i] = xx[i];
+            lastf[i] = ff[i];
+        }
+        Epot0 = Epot;
+
+        first = TRUE;
+
+        for (i = 0; i < n; i++)
+        {
+            xa[i] = xx[i];
+        }
+
+        /* Take a step downhill.
+         * In theory, we should minimize the function along this direction.
+         * That is quite possible, but it turns out to take 5-10 function evaluations
+         * for each line. However, we dont really need to find the exact minimum -
+         * it is much better to start a new BFGS step in a modified direction as soon
+         * as we are close to it. This will save a lot of energy evaluations.
+         *
+         * In practice, we just try to take a single step.
+         * If it worked (i.e. lowered the energy), we increase the stepsize but
+         * the continue straight to the next BFGS step without trying to find any minimum.
+         * If it didn't work (higher energy), there must be a minimum somewhere between
+         * the old position and the new one.
+         *
+         * Due to the finite numerical accuracy, it turns out that it is a good idea
+         * to even accept a SMALL increase in energy, if the derivative is still downhill.
+         * This leads to lower final energies in the tests I've done. / Erik
+         */
+        foundlower = FALSE;
+        EpotA      = Epot0;
+        a          = 0.0;
+        c          = a + stepsize; /* reference position along line is zero */
+
+        /* Check stepsize first. We do not allow displacements
+         * larger than emstep.
+         */
+        do
+        {
+            c        = a + stepsize;
+            maxdelta = 0;
+            for (i = 0; i < n; i++)
+            {
+                delta = c*s[i];
+                if (delta > maxdelta)
+                {
+                    maxdelta = delta;
+                }
+            }
+            if (maxdelta > inputrec->em_stepsize)
+            {
+                stepsize *= 0.1;
+            }
+        }
+        while (maxdelta > inputrec->em_stepsize);
+
+        /* Take a trial step */
+        for (i = 0; i < n; i++)
+        {
+            xc[i] = lastx[i] + c*s[i];
+        }
+
+        neval++;
+        /* Calculate energy for the trial step */
+        ems.s.x = (rvec *)xc;
+        ems.f   = (rvec *)fc;
+        evaluate_energy(fplog, cr,
+                        top_global, &ems, top,
+                        inputrec, nrnb, wcycle, gstat,
+                        vsite, constr, fcd, graph, mdatoms, fr,
+                        mu_tot, enerd, vir, pres, step, FALSE);
+        EpotC = ems.epot;
+
+        /* Calc derivative along line */
+        for (gpc = 0, i = 0; i < n; i++)
+        {
+            gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
+        }
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr))
+        {
+            gmx_sumd(1, &gpc, cr);
+        }
+
+        /* This is the max amount of increase in energy we tolerate */
+        tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
+
+        /* Accept the step if the energy is lower, or if it is not significantly higher
+         * and the line derivative is still negative.
+         */
+        if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
+        {
+            foundlower = TRUE;
+            /* Great, we found a better energy. Increase step for next iteration
+             * if we are still going down, decrease it otherwise
+             */
+            if (gpc < 0)
+            {
+                stepsize *= 1.618034; /* The golden section */
+            }
+            else
+            {
+                stepsize *= 0.618034; /* 1/golden section */
+            }
+        }
+        else
+        {
+            /* New energy is the same or higher. We will have to do some work
+             * to find a smaller value in the interval. Take smaller step next time!
+             */
+            foundlower = FALSE;
+            stepsize  *= 0.618034;
+        }
+
+        /* OK, if we didn't find a lower value we will have to locate one now - there must
+         * be one in the interval [a=0,c].
+         * The same thing is valid here, though: Don't spend dozens of iterations to find
+         * the line minimum. We try to interpolate based on the derivative at the endpoints,
+         * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+         *
+         * I also have a safeguard for potentially really patological functions so we never
+         * take more than 20 steps before we give up ...
+         *
+         * If we already found a lower value we just skip this step and continue to the update.
+         */
+
+        if (!foundlower)
+        {
+
+            nminstep = 0;
+            do
+            {
+                /* Select a new trial point.
+                 * If the derivatives at points a & c have different sign we interpolate to zero,
+                 * otherwise just do a bisection.
+                 */
+
+                if (gpa < 0 && gpc > 0)
+                {
+                    b = a + gpa*(a-c)/(gpc-gpa);
+                }
+                else
+                {
+                    b = 0.5*(a+c);
+                }
+
+                /* safeguard if interpolation close to machine accuracy causes errors:
+                 * never go outside the interval
+                 */
+                if (b <= a || b >= c)
+                {
+                    b = 0.5*(a+c);
+                }
+
+                /* Take a trial step */
+                for (i = 0; i < n; i++)
+                {
+                    xb[i] = lastx[i] + b*s[i];
+                }
+
+                neval++;
+                /* Calculate energy for the trial step */
+                ems.s.x = (rvec *)xb;
+                ems.f   = (rvec *)fb;
+                evaluate_energy(fplog, cr,
+                                top_global, &ems, top,
+                                inputrec, nrnb, wcycle, gstat,
+                                vsite, constr, fcd, graph, mdatoms, fr,
+                                mu_tot, enerd, vir, pres, step, FALSE);
+                EpotB = ems.epot;
+
+                fnorm = ems.fnorm;
+
+                for (gpb = 0, i = 0; i < n; i++)
+                {
+                    gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
+
+                }
+                /* Sum the gradient along the line across CPUs */
+                if (PAR(cr))
+                {
+                    gmx_sumd(1, &gpb, cr);
+                }
+
+                /* Keep one of the intervals based on the value of the derivative at the new point */
+                if (gpb > 0)
+                {
+                    /* Replace c endpoint with b */
+                    EpotC = EpotB;
+                    c     = b;
+                    gpc   = gpb;
+                    /* swap coord pointers b/c */
+                    xtmp = xb;
+                    ftmp = fb;
+                    xb   = xc;
+                    fb   = fc;
+                    xc   = xtmp;
+                    fc   = ftmp;
+                }
+                else
+                {
+                    /* Replace a endpoint with b */
+                    EpotA = EpotB;
+                    a     = b;
+                    gpa   = gpb;
+                    /* swap coord pointers a/b */
+                    xtmp = xb;
+                    ftmp = fb;
+                    xb   = xa;
+                    fb   = fa;
+                    xa   = xtmp;
+                    fa   = ftmp;
+                }
+
+                /*
+                 * Stop search as soon as we find a value smaller than the endpoints,
+                 * or if the tolerance is below machine precision.
+                 * Never run more than 20 steps, no matter what.
+                 */
+                nminstep++;
+            }
+            while ((EpotB > EpotA || EpotB > EpotC) && (nminstep < 20));
+
+            if (fabs(EpotB-Epot0) < GMX_REAL_EPS || nminstep >= 20)
+            {
+                /* OK. We couldn't find a significantly lower energy.
+                 * If ncorr==0 this was steepest descent, and then we give up.
+                 * If not, reset memory to restart as steepest descent before quitting.
+                 */
+                if (ncorr == 0)
+                {
+                    /* Converged */
+                    converged = TRUE;
+                    break;
+                }
+                else
+                {
+                    /* Reset memory */
+                    ncorr = 0;
+                    /* Search in gradient direction */
+                    for (i = 0; i < n; i++)
+                    {
+                        dx[point][i] = ff[i];
+                    }
+                    /* Reset stepsize */
+                    stepsize = 1.0/fnorm;
+                    continue;
+                }
+            }
+
+            /* Select min energy state of A & C, put the best in xx/ff/Epot
+             */
+            if (EpotC < EpotA)
+            {
+                Epot = EpotC;
+                /* Use state C */
+                for (i = 0; i < n; i++)
+                {
+                    xx[i] = xc[i];
+                    ff[i] = fc[i];
+                }
+                stepsize = c;
+            }
+            else
+            {
+                Epot = EpotA;
+                /* Use state A */
+                for (i = 0; i < n; i++)
+                {
+                    xx[i] = xa[i];
+                    ff[i] = fa[i];
+                }
+                stepsize = a;
+            }
+
+        }
+        else
+        {
+            /* found lower */
+            Epot = EpotC;
+            /* Use state C */
+            for (i = 0; i < n; i++)
+            {
+                xx[i] = xc[i];
+                ff[i] = fc[i];
+            }
+            stepsize = c;
+        }
+
+        /* Update the memory information, and calculate a new
+         * approximation of the inverse hessian
+         */
+
+        /* Have new data in Epot, xx, ff */
+        if (ncorr < nmaxcorr)
+        {
+            ncorr++;
+        }
+
+        for (i = 0; i < n; i++)
+        {
+            dg[point][i]  = lastf[i]-ff[i];
+            dx[point][i] *= stepsize;
+        }
+
+        dgdg = 0;
+        dgdx = 0;
+        for (i = 0; i < n; i++)
+        {
+            dgdg += dg[point][i]*dg[point][i];
+            dgdx += dg[point][i]*dx[point][i];
+        }
+
+        diag = dgdx/dgdg;
+
+        rho[point] = 1.0/dgdx;
+        point++;
+
+        if (point >= nmaxcorr)
+        {
+            point = 0;
+        }
+
+        /* Update */
+        for (i = 0; i < n; i++)
+        {
+            p[i] = ff[i];
+        }
+
+        cp = point;
+
+        /* Recursive update. First go back over the memory points */
+        for (k = 0; k < ncorr; k++)
+        {
+            cp--;
+            if (cp < 0)
+            {
+                cp = ncorr-1;
+            }
+
+            sq = 0;
+            for (i = 0; i < n; i++)
+            {
+                sq += dx[cp][i]*p[i];
+            }
+
+            alpha[cp] = rho[cp]*sq;
+
+            for (i = 0; i < n; i++)
+            {
+                p[i] -= alpha[cp]*dg[cp][i];
+            }
+        }
+
+        for (i = 0; i < n; i++)
+        {
+            p[i] *= diag;
+        }
+
+        /* And then go forward again */
+        for (k = 0; k < ncorr; k++)
+        {
+            yr = 0;
+            for (i = 0; i < n; i++)
+            {
+                yr += p[i]*dg[cp][i];
+            }
+
+            beta = rho[cp]*yr;
+            beta = alpha[cp]-beta;
+
+            for (i = 0; i < n; i++)
+            {
+                p[i] += beta*dx[cp][i];
+            }
+
+            cp++;
+            if (cp >= ncorr)
+            {
+                cp = 0;
+            }
+        }
+
+        for (i = 0; i < n; i++)
+        {
+            if (!frozen[i])
+            {
+                dx[point][i] = p[i];
+            }
+            else
+            {
+                dx[point][i] = 0;
+            }
+        }
+
+        stepsize = 1.0;
+
+        /* Test whether the convergence criterion is met */
+        get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
+
+        /* Print it if necessary */
+        if (MASTER(cr))
+        {
+            if (bVerbose)
+            {
+                fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+                        step, Epot, fnorm/sqrt(state->natoms), fmax, nfmax+1);
+            }
+            /* Store the new (lower) energies */
+            upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+                       mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+                       NULL, NULL, vir, pres, NULL, mu_tot, constr);
+            do_log = do_per_step(step, inputrec->nstlog);
+            do_ene = do_per_step(step, inputrec->nstenergy);
+            if (do_log)
+            {
+                print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+            }
+            print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+                       do_log ? fplog : NULL, step, step, eprNORMAL,
+                       TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+        }
+
+        /* Send x and E to IMD client, if bIMD is TRUE. */
+        if (do_IMD(inputrec->bIMD, step, cr, TRUE, state->box, state->x, inputrec, 0, wcycle) && MASTER(cr))
+        {
+            IMD_send_positions(inputrec->imd);
+        }
+
+        /* Stop when the maximum force lies below tolerance.
+         * If we have reached machine precision, converged is already set to true.
+         */
+
+        converged = converged || (fmax < inputrec->em_tol);
+
+    } /* End of the loop */
+
+    /* IMD cleanup, if bIMD is TRUE. */
+    IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+    if (converged)
+    {
+        step--; /* we never took that last step in this case */
+
+    }
+    if (fmax > inputrec->em_tol)
+    {
+        if (MASTER(cr))
+        {
+            warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
+            warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
+        }
+        converged = FALSE;
+    }
+
+    /* If we printed energy and/or logfile last step (which was the last step)
+     * we don't have to do it again, but otherwise print the final values.
+     */
+    if (!do_log) /* Write final value to log since we didn't do anythin last step */
+    {
+        print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+    }
+    if (!do_ene || !do_log) /* Write final energy file entries */
+    {
+        print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+                   !do_log ? fplog : NULL, step, step, eprNORMAL,
+                   TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+    }
+
+    /* Print some stuff... */
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+
+    /* IMPORTANT!
+     * For accurate normal mode calculation it is imperative that we
+     * store the last conformation into the full precision binary trajectory.
+     *
+     * However, we should only do it if we did NOT already write this step
+     * above (which we did if do_x or do_f was true).
+     */
+    do_x = !do_per_step(step, inputrec->nstxout);
+    do_f = !do_per_step(step, inputrec->nstfout);
+    write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+                  top_global, inputrec, step,
+                  &ems, state, f);
+
+    if (MASTER(cr))
+    {
+        print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
+                        number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+        print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
+                        number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+
+        fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+    }
+
+    finish_em(cr, outf, walltime_accounting, wcycle);
+
+    /* To print the actual number of steps we needed somewhere */
+    walltime_accounting_set_nsteps_done(walltime_accounting, step);
+
+    return 0;
+} /* That's all folks */
+
+
+double do_steep(FILE *fplog, t_commrec *cr,
+                int nfile, const t_filenm fnm[],
+                const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+                int gmx_unused nstglobalcomm,
+                gmx_vsite_t *vsite, gmx_constr_t constr,
+                int gmx_unused stepout,
+                t_inputrec *inputrec,
+                gmx_mtop_t *top_global, t_fcdata *fcd,
+                t_state *state_global,
+                t_mdatoms *mdatoms,
+                t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+                gmx_edsam_t gmx_unused  ed,
+                t_forcerec *fr,
+                int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+                gmx_membed_t gmx_unused membed,
+                real gmx_unused cpt_period, real gmx_unused max_hours,
+                const char  gmx_unused *deviceOptions,
+                int imdport,
+                unsigned long gmx_unused Flags,
+                gmx_walltime_accounting_t walltime_accounting)
+{
+    const char       *SD = "Steepest Descents";
+    em_state_t       *s_min, *s_try;
+    rvec             *f_global;
+    gmx_localtop_t   *top;
+    gmx_enerdata_t   *enerd;
+    rvec             *f;
+    gmx_global_stat_t gstat;
+    t_graph          *graph;
+    real              stepsize, constepsize;
+    real              ustep, fnormn;
+    gmx_mdoutf_t      outf;
+    t_mdebin         *mdebin;
+    gmx_bool          bDone, bAbort, do_x, do_f;
+    tensor            vir, pres;
+    rvec              mu_tot;
+    int               nsteps;
+    int               count          = 0;
+    int               steps_accepted = 0;
+    /* not used */
+    real              terminate = 0;
+
+    s_min = init_em_state();
+    s_try = init_em_state();
+
+    /* Init em and store the local state in s_try */
+    init_em(fplog, SD, cr, inputrec,
+            state_global, top_global, s_try, &top, &f, &f_global,
+            nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+
+    /* Print to log file  */
+    print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
+
+    /* Set variables for stepsize (in nm). This is the largest
+     * step that we are going to make in any direction.
+     */
+    ustep    = inputrec->em_stepsize;
+    stepsize = 0;
+
+    /* Max number of steps  */
+    nsteps = inputrec->nsteps;
+
+    if (MASTER(cr))
+    {
+        /* Print to the screen  */
+        sp_header(stderr, SD, inputrec->em_tol, nsteps);
+    }
+    if (fplog)
+    {
+        sp_header(fplog, SD, inputrec->em_tol, nsteps);
+    }
+
+    /**** HERE STARTS THE LOOP ****
+     * count is the counter for the number of steps
+     * bDone will be TRUE when the minimization has converged
+     * bAbort will be TRUE when nsteps steps have been performed or when
+     * the stepsize becomes smaller than is reasonable for machine precision
+     */
+    count  = 0;
+    bDone  = FALSE;
+    bAbort = FALSE;
+    while (!bDone && !bAbort)
+    {
+        bAbort = (nsteps >= 0) && (count == nsteps);
+
+        /* set new coordinates, except for first step */
+        if (count > 0)
+        {
+            do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
+                       s_min, stepsize, s_min->f, s_try,
+                       constr, top, nrnb, wcycle, count);
+        }
+
+        evaluate_energy(fplog, cr,
+                        top_global, s_try, top,
+                        inputrec, nrnb, wcycle, gstat,
+                        vsite, constr, fcd, graph, mdatoms, fr,
+                        mu_tot, enerd, vir, pres, count, count == 0);
+
+        if (MASTER(cr))
+        {
+            print_ebin_header(fplog, count, count, s_try->s.lambda[efptFEP]);
+        }
+
+        if (count == 0)
+        {
+            s_min->epot = s_try->epot + 1;
+        }
+
+        /* Print it if necessary  */
+        if (MASTER(cr))
+        {
+            if (bVerbose)
+            {
+                fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
+                        count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
+                        (s_try->epot < s_min->epot) ? '\n' : '\r');
+            }
+
+            if (s_try->epot < s_min->epot)
+            {
+                /* Store the new (lower) energies  */
+                upd_mdebin(mdebin, FALSE, FALSE, (double)count,
+                           mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
+                           s_try->s.box, NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+                /* Prepare IMD energy record, if bIMD is TRUE. */
+                IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
+
+                print_ebin(mdoutf_get_fp_ene(outf), TRUE,
+                           do_per_step(steps_accepted, inputrec->nstdisreout),
+                           do_per_step(steps_accepted, inputrec->nstorireout),
+                           fplog, count, count, eprNORMAL, TRUE,
+                           mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+                fflush(fplog);
+            }
+        }
+
+        /* Now if the new energy is smaller than the previous...
+         * or if this is the first step!
+         * or if we did random steps!
+         */
+
+        if ( (count == 0) || (s_try->epot < s_min->epot) )
+        {
+            steps_accepted++;
+
+            /* Test whether the convergence criterion is met...  */
+            bDone = (s_try->fmax < inputrec->em_tol);
+
+            /* Copy the arrays for force, positions and energy  */
+            /* The 'Min' array always holds the coords and forces of the minimal
+               sampled energy  */
+            swap_em_state(s_min, s_try);
+            if (count > 0)
+            {
+                ustep *= 1.2;
+            }
+
+            /* Write to trn, if necessary */
+            do_x = do_per_step(steps_accepted, inputrec->nstxout);
+            do_f = do_per_step(steps_accepted, inputrec->nstfout);
+            write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+                          top_global, inputrec, count,
+                          s_min, state_global, f_global);
+        }
+        else
+        {
+            /* If energy is not smaller make the step smaller...  */
+            ustep *= 0.5;
+
+            if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+            {
+                /* Reload the old state */
+                em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+                                       s_min, top, mdatoms, fr, vsite, constr,
+                                       nrnb, wcycle);
+            }
+        }
+
+        /* Determine new step  */
+        stepsize = ustep/s_min->fmax;
+
+        /* Check if stepsize is too small, with 1 nm as a characteristic length */
+#ifdef GMX_DOUBLE
+        if (count == nsteps || ustep < 1e-12)
+#else
+        if (count == nsteps || ustep < 1e-6)
+#endif
+        {
+            if (MASTER(cr))
+            {
+                warn_step(stderr, inputrec->em_tol, count == nsteps, constr != NULL);
+                warn_step(fplog, inputrec->em_tol, count == nsteps, constr != NULL);
+            }
+            bAbort = TRUE;
+        }
+
+        /* Send IMD energies and positions, if bIMD is TRUE. */
+        if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+        {
+            IMD_send_positions(inputrec->imd);
+        }
+
+        count++;
+    } /* End of the loop  */
+
+    /* IMD cleanup, if bIMD is TRUE. */
+    IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+    /* Print some data...  */
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+    write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
+                  top_global, inputrec, count,
+                  s_min, state_global, f_global);
+
+    fnormn = s_min->fnorm/sqrt(state_global->natoms);
+
+    if (MASTER(cr))
+    {
+        print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
+                        s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+        print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
+                        s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+    }
+
+    finish_em(cr, outf, walltime_accounting, wcycle);
+
+    /* To print the actual number of steps we needed somewhere */
+    inputrec->nsteps = count;
+
+    walltime_accounting_set_nsteps_done(walltime_accounting, count);
+
+    return 0;
+} /* That's all folks */
+
+
+double do_nm(FILE *fplog, t_commrec *cr,
+             int nfile, const t_filenm fnm[],
+             const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused  bCompact,
+             int gmx_unused nstglobalcomm,
+             gmx_vsite_t *vsite, gmx_constr_t constr,
+             int gmx_unused stepout,
+             t_inputrec *inputrec,
+             gmx_mtop_t *top_global, t_fcdata *fcd,
+             t_state *state_global,
+             t_mdatoms *mdatoms,
+             t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+             gmx_edsam_t  gmx_unused ed,
+             t_forcerec *fr,
+             int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+             gmx_membed_t gmx_unused membed,
+             real gmx_unused cpt_period, real gmx_unused max_hours,
+             const char gmx_unused *deviceOptions,
+             int imdport,
+             unsigned long gmx_unused Flags,
+             gmx_walltime_accounting_t walltime_accounting)
+{
+    const char          *NM = "Normal Mode Analysis";
+    gmx_mdoutf_t         outf;
+    int                  natoms, atom, d;
+    int                  nnodes, node;
+    rvec                *f_global;
+    gmx_localtop_t      *top;
+    gmx_enerdata_t      *enerd;
+    rvec                *f;
+    gmx_global_stat_t    gstat;
+    t_graph             *graph;
+    real                 t, t0, lambda, lam0;
+    gmx_bool             bNS;
+    tensor               vir, pres;
+    rvec                 mu_tot;
+    rvec                *fneg, *dfdx;
+    gmx_bool             bSparse; /* use sparse matrix storage format */
+    size_t               sz = 0;
+    gmx_sparsematrix_t * sparse_matrix           = NULL;
+    real           *     full_matrix             = NULL;
+    em_state_t       *   state_work;
+
+    /* added with respect to mdrun */
+    int        i, j, k, row, col;
+    real       der_range = 10.0*sqrt(GMX_REAL_EPS);
+    real       x_min;
+    real       fnorm, fmax;
+
+    if (constr != NULL)
+    {
+        gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
+    }
+
+    state_work = init_em_state();
+
+    /* Init em and store the local state in state_minimum */
+    init_em(fplog, NM, cr, inputrec,
+            state_global, top_global, state_work, &top,
+            &f, &f_global,
+            nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+            nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
+
+    natoms = top_global->natoms;
+    snew(fneg, natoms);
+    snew(dfdx, natoms);
+
+#ifndef GMX_DOUBLE
+    if (MASTER(cr))
+    {
+        fprintf(stderr,
+                "NOTE: This version of Gromacs has been compiled in single precision,\n"
+                "      which MIGHT not be accurate enough for normal mode analysis.\n"
+                "      Gromacs now uses sparse matrix storage, so the memory requirements\n"
+                "      are fairly modest even if you recompile in double precision.\n\n");
+    }
+#endif
+
+    /* Check if we can/should use sparse storage format.
+     *
+     * Sparse format is only useful when the Hessian itself is sparse, which it
+     * will be when we use a cutoff.
+     * For small systems (n<1000) it is easier to always use full matrix format, though.
+     */
+    if (EEL_FULL(fr->eeltype) || fr->rlist == 0.0)
+    {
+        md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
+        bSparse = FALSE;
+    }
+    else if (top_global->natoms < 1000)
+    {
+        md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", top_global->natoms);
+        bSparse = FALSE;
+    }
+    else
+    {
+        md_print_info(cr, fplog, "Using compressed symmetric sparse Hessian format.\n");
+        bSparse = TRUE;
+    }
+
+    if (MASTER(cr))
+    {
+        sz = DIM*top_global->natoms;
+
+        fprintf(stderr, "Allocating Hessian memory...\n\n");
+
+        if (bSparse)
+        {
+            sparse_matrix = gmx_sparsematrix_init(sz);
+            sparse_matrix->compressed_symmetric = TRUE;
+        }
+        else
+        {
+            snew(full_matrix, sz*sz);
+        }
+    }
+
+    /* Initial values */
+    t0           = inputrec->init_t;
+    lam0         = inputrec->fepvals->init_lambda;
+    t            = t0;
+    lambda       = lam0;
+
+    init_nrnb(nrnb);
+
+    where();
+
+    /* Write start time and temperature */
+    print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
+
+    /* fudge nr of steps to nr of atoms */
+    inputrec->nsteps = natoms*2;
+
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
+                *(top_global->name), (int)inputrec->nsteps);
+    }
+
+    nnodes = cr->nnodes;
+
+    /* Make evaluate_energy do a single node force calculation */
+    cr->nnodes = 1;
+    evaluate_energy(fplog, cr,
+                    top_global, state_work, top,
+                    inputrec, nrnb, wcycle, gstat,
+                    vsite, constr, fcd, graph, mdatoms, fr,
+                    mu_tot, enerd, vir, pres, -1, TRUE);
+    cr->nnodes = nnodes;
+
+    /* if forces are not small, warn user */
+    get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, state_work);
+
+    md_print_info(cr, fplog, "Maximum force:%12.5e\n", state_work->fmax);
+    if (state_work->fmax > 1.0e-3)
+    {
+        md_print_info(cr, fplog,
+                      "The force is probably not small enough to "
+                      "ensure that you are at a minimum.\n"
+                      "Be aware that negative eigenvalues may occur\n"
+                      "when the resulting matrix is diagonalized.\n\n");
+    }
+
+    /***********************************************************
+     *
+     *      Loop over all pairs in matrix
+     *
+     *      do_force called twice. Once with positive and
+     *      once with negative displacement
+     *
+     ************************************************************/
+
+    /* Steps are divided one by one over the nodes */
+    for (atom = cr->nodeid; atom < natoms; atom += nnodes)
+    {
+
+        for (d = 0; d < DIM; d++)
+        {
+            x_min = state_work->s.x[atom][d];
+
+            state_work->s.x[atom][d] = x_min - der_range;
+
+            /* Make evaluate_energy do a single node force calculation */
+            cr->nnodes = 1;
+            evaluate_energy(fplog, cr,
+                            top_global, state_work, top,
+                            inputrec, nrnb, wcycle, gstat,
+                            vsite, constr, fcd, graph, mdatoms, fr,
+                            mu_tot, enerd, vir, pres, atom*2, FALSE);
+
+            for (i = 0; i < natoms; i++)
+            {
+                copy_rvec(state_work->f[i], fneg[i]);
+            }
+
+            state_work->s.x[atom][d] = x_min + der_range;
+
+            evaluate_energy(fplog, cr,
+                            top_global, state_work, top,
+                            inputrec, nrnb, wcycle, gstat,
+                            vsite, constr, fcd, graph, mdatoms, fr,
+                            mu_tot, enerd, vir, pres, atom*2+1, FALSE);
+            cr->nnodes = nnodes;
+
+            /* x is restored to original */
+            state_work->s.x[atom][d] = x_min;
+
+            for (j = 0; j < natoms; j++)
+            {
+                for (k = 0; (k < DIM); k++)
+                {
+                    dfdx[j][k] =
+                        -(state_work->f[j][k] - fneg[j][k])/(2*der_range);
+                }
+            }
+
+            if (!MASTER(cr))
+            {
+#ifdef GMX_MPI
+#ifdef GMX_DOUBLE
+#define mpi_type MPI_DOUBLE
+#else
+#define mpi_type MPI_FLOAT
+#endif
+                MPI_Send(dfdx[0], natoms*DIM, mpi_type, MASTERNODE(cr), cr->nodeid,
+                         cr->mpi_comm_mygroup);
+#endif
+            }
+            else
+            {
+                for (node = 0; (node < nnodes && atom+node < natoms); node++)
+                {
+                    if (node > 0)
+                    {
+#ifdef GMX_MPI
+                        MPI_Status stat;
+                        MPI_Recv(dfdx[0], natoms*DIM, mpi_type, node, node,
+                                 cr->mpi_comm_mygroup, &stat);
+#undef mpi_type
+#endif
+                    }
+
+                    row = (atom + node)*DIM + d;
+
+                    for (j = 0; j < natoms; j++)
+                    {
+                        for (k = 0; k < DIM; k++)
+                        {
+                            col = j*DIM + k;
+
+                            if (bSparse)
+                            {
+                                if (col >= row && dfdx[j][k] != 0.0)
+                                {
+                                    gmx_sparsematrix_increment_value(sparse_matrix,
+                                                                     row, col, dfdx[j][k]);
+                                }
+                            }
+                            else
+                            {
+                                full_matrix[row*sz+col] = dfdx[j][k];
+                            }
+                        }
+                    }
+                }
+            }
+
+            if (bVerbose && fplog)
+            {
+                fflush(fplog);
+            }
+        }
+        /* write progress */
+        if (MASTER(cr) && bVerbose)
+        {
+            fprintf(stderr, "\rFinished step %d out of %d",
+                    min(atom+nnodes, natoms), natoms);
+            fflush(stderr);
+        }
+    }
+
+    if (MASTER(cr))
+    {
+        fprintf(stderr, "\n\nWriting Hessian...\n");
+        gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
+    }
+
+    finish_em(cr, outf, walltime_accounting, wcycle);
+
+    walltime_accounting_set_nsteps_done(walltime_accounting, natoms*2);
+
+    return 0;
+}
diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index 3d98d59..b34d23c 100644
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -96,6 +96,12 @@
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/imd/imd.h"
 
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
 #ifdef GMX_FAHCORE
 #include "corewrap.h"
 #endif
@@ -224,6 +230,12 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     /* Interactive MD */
     gmx_bool          bIMDstep = FALSE;
 
+    /* PLUMED */
+    int plumedNeedsEnergy=0;
+    int plumedWantsToStop=0;
+    matrix plumed_vir;
+    /* END PLUMED */
+
 #ifdef GMX_FAHCORE
     /* Temporary addition for FAHCORE checkpointing */
     int chkpt_ret;
@@ -651,6 +663,48 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
         fprintf(fplog, "\n");
     }
 
+    /* PLUMED */
+    if(plumedswitch){
+      /* detect plumed API version */
+      int pversion=0;
+      plumed_cmd(plumedmain,"getApiVersion",&pversion);
+      /* setting kbT is only implemented with api>1) */
+      real kbT=ir->opts.ref_t[0]*BOLTZ;
+      if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT);
+
+      if(cr->ms && cr->ms->nsim>1) {
+        if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
+        if(PAR(cr)){
+          if(DOMAINDECOMP(cr)) {
+            plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
+          }else{
+            plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
+          }
+        }
+        plumed_cmd(plumedmain,"GREX init",NULL);
+      }
+      if(PAR(cr)){
+        if(DOMAINDECOMP(cr)) {
+          plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+        }
+      }
+      plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
+      plumed_cmd(plumedmain,"setMDEngine","gromacs");
+      plumed_cmd(plumedmain,"setLog",fplog);
+      real real_delta_t;
+      real_delta_t=ir->delta_t;
+      plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
+      plumed_cmd(plumedmain,"init",NULL);
+
+      if(PAR(cr)){
+        if(DOMAINDECOMP(cr)) {
+          plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+          plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+        }
+      }
+    }
+    /* END PLUMED */
+
     walltime_accounting_start(walltime_accounting);
     wallcycle_start(wcycle, ewcRUN);
     print_start(fplog, cr, walltime_accounting, "mdrun");
@@ -955,6 +1009,13 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                                     do_verbose && !bPMETuneRunning);
                 wallcycle_stop(wcycle, ewcDOMDEC);
                 /* If using an iterative integrator, reallocate space to match the decomposition */
+
+                /* PLUMED */
+                if(plumedswitch){
+                  plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+                  plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+                }
+                /* END PLUMED */
             }
         }
 
@@ -1078,12 +1139,45 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
              * This is parallellized as well, and does communication too.
              * Check comments in sim_util.c
              */
+
+            /* PLUMED */
+            plumedNeedsEnergy=0;
+            if(plumedswitch){
+              long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
+              plumed_cmd(plumedmain,"setPositions",&state->x[0][0]);
+              plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[0]);
+              plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[0]);
+              plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
+              plumed_cmd(plumedmain,"prepareCalc",NULL);
+              plumed_cmd(plumedmain,"setStopFlag",&plumedWantsToStop);
+              plumed_cmd(plumedmain,"setForces",&f[0][0]);
+              plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+              clear_mat(plumed_vir);
+              plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
+            }
+            /* END PLUMED */
             do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
                      state->box, state->x, &state->hist,
                      f, force_vir, mdatoms, enerd, fcd,
                      state->lambda, graph,
                      fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
                      (bNS ? GMX_FORCE_NS : 0) | force_flags);
+            /* PLUMED */
+            if(plumedswitch){
+              if(plumedNeedsEnergy){
+                msmul(force_vir,2.0,plumed_vir);
+                plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
+                plumed_cmd(plumedmain,"performCalc",NULL);
+                msmul(plumed_vir,0.5,force_vir);
+              } else {
+                msmul(plumed_vir,0.5,plumed_vir);
+                m_add(force_vir,plumed_vir,force_vir);
+              }
+              if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+                 do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
+              if(plumedWantsToStop) ir->nsteps=step_rel+1;
+            }
+            /* END PLUMED */
         }
 
         if (bVV && !bStartingFromCpt && !bRerunMD)
diff --git a/src/programs/mdrun/md.c.preplumed b/src/programs/mdrun/md.c.preplumed
new file mode 100644
index 0000000..3d98d59
--- /dev/null
+++ b/src/programs/mdrun/md.c.preplumed
@@ -0,0 +1,2058 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "vcm.h"
+#include "mdebin.h"
+#include "nrnb.h"
+#include "calcmu.h"
+#include "index.h"
+#include "vsite.h"
+#include "update.h"
+#include "ns.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "network.h"
+#include "xvgr.h"
+#include "physics.h"
+#include "names.h"
+#include "force.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "deform.h"
+#include "qmmm.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "gromacs/gmxlib/topsort.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "shellfc.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "txtdump.h"
+#include "gromacs/utility/cstringutil.h"
+#include "pme_loadbal.h"
+#include "bondf.h"
+#include "membed.h"
+#include "types/nlistheuristics.h"
+#include "types/iteratedconstraints.h"
+#include "nbnxn_cuda_data_mgmt.h"
+
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/imd/imd.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+static void reset_all_counters(FILE *fplog, t_commrec *cr,
+                               gmx_int64_t step,
+                               gmx_int64_t *step_rel, t_inputrec *ir,
+                               gmx_wallcycle_t wcycle, t_nrnb *nrnb,
+                               gmx_walltime_accounting_t walltime_accounting,
+                               nbnxn_cuda_ptr_t cu_nbv)
+{
+    char sbuf[STEPSTRSIZE];
+
+    /* Reset all the counters related to performance over the run */
+    md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
+                  gmx_step_str(step, sbuf));
+
+    if (cu_nbv)
+    {
+        nbnxn_cuda_reset_timings(cu_nbv);
+    }
+
+    wallcycle_stop(wcycle, ewcRUN);
+    wallcycle_reset_all(wcycle);
+    if (DOMAINDECOMP(cr))
+    {
+        reset_dd_statistics_counters(cr->dd);
+    }
+    init_nrnb(nrnb);
+    ir->init_step += *step_rel;
+    ir->nsteps    -= *step_rel;
+    *step_rel      = 0;
+    wallcycle_start(wcycle, ewcRUN);
+    walltime_accounting_start(walltime_accounting);
+    print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
+}
+
+double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
+             const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
+             int nstglobalcomm,
+             gmx_vsite_t *vsite, gmx_constr_t constr,
+             int stepout, t_inputrec *ir,
+             gmx_mtop_t *top_global,
+             t_fcdata *fcd,
+             t_state *state_global,
+             t_mdatoms *mdatoms,
+             t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+             gmx_edsam_t ed, t_forcerec *fr,
+             int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
+             real cpt_period, real max_hours,
+             const char gmx_unused *deviceOptions,
+             int imdport,
+             unsigned long Flags,
+             gmx_walltime_accounting_t walltime_accounting)
+{
+    gmx_mdoutf_t    outf = NULL;
+    gmx_int64_t     step, step_rel;
+    double          elapsed_time;
+    double          t, t0, lam0[efptNR];
+    gmx_bool        bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+    gmx_bool        bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
+                    bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
+                    bBornRadii, bStartingFromCpt;
+    gmx_bool          bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
+    gmx_bool          do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
+                      bForceUpdate = FALSE, bCPT;
+    gmx_bool          bMasterState;
+    int               force_flags, cglo_flags;
+    tensor            force_vir, shake_vir, total_vir, tmp_vir, pres;
+    int               i, m;
+    t_trxstatus      *status;
+    rvec              mu_tot;
+    t_vcm            *vcm;
+    t_state          *bufstate = NULL;
+    matrix           *scale_tot, pcoupl_mu, M, ebox;
+    gmx_nlheur_t      nlh;
+    t_trxframe        rerun_fr;
+    gmx_repl_ex_t     repl_ex = NULL;
+    int               nchkpt  = 1;
+    gmx_localtop_t   *top;
+    t_mdebin         *mdebin   = NULL;
+    t_state          *state    = NULL;
+    rvec             *f_global = NULL;
+    gmx_enerdata_t   *enerd;
+    rvec             *f = NULL;
+    gmx_global_stat_t gstat;
+    gmx_update_t      upd   = NULL;
+    t_graph          *graph = NULL;
+    globsig_t         gs;
+    gmx_groups_t     *groups;
+    gmx_ekindata_t   *ekind, *ekind_save;
+    gmx_shellfc_t     shellfc;
+    int               count, nconverged = 0;
+    real              timestep   = 0;
+    double            tcount     = 0;
+    gmx_bool          bConverged = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
+    gmx_bool          bAppend;
+    gmx_bool          bResetCountersHalfMaxH = FALSE;
+    gmx_bool          bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+    gmx_bool          bUpdateDoLR;
+    real              dvdl_constr;
+    rvec             *cbuf = NULL;
+    matrix            lastbox;
+    real              veta_save, scalevir, tracevir;
+    real              vetanew = 0;
+    int               lamnew  = 0;
+    /* for FEP */
+    int               nstfep;
+    double            cycles;
+    real              saved_conserved_quantity = 0;
+    real              last_ekin                = 0;
+    int               iter_i;
+    t_extmass         MassQ;
+    int             **trotter_seq;
+    char              sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
+    int               handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
+    gmx_iterate_t     iterate;
+    gmx_int64_t       multisim_nsteps = -1;                        /* number of steps to do  before first multisim
+                                                                          simulation stops. If equal to zero, don't
+                                                                          communicate any more between multisims.*/
+    /* PME load balancing data for GPU kernels */
+    pme_load_balancing_t pme_loadbal = NULL;
+    double               cycles_pmes;
+    gmx_bool             bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
+
+    /* Interactive MD */
+    gmx_bool          bIMDstep = FALSE;
+
+#ifdef GMX_FAHCORE
+    /* Temporary addition for FAHCORE checkpointing */
+    int chkpt_ret;
+#endif
+
+    /* Check for special mdrun options */
+    bRerunMD = (Flags & MD_RERUN);
+    bAppend  = (Flags & MD_APPENDFILES);
+    if (Flags & MD_RESETCOUNTERSHALFWAY)
+    {
+        if (ir->nsteps > 0)
+        {
+            /* Signal to reset the counters half the simulation steps. */
+            wcycle_set_reset_counters(wcycle, ir->nsteps/2);
+        }
+        /* Signal to reset the counters halfway the simulation time. */
+        bResetCountersHalfMaxH = (max_hours > 0);
+    }
+
+    /* md-vv uses averaged full step velocities for T-control
+       md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
+       md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
+    bVV = EI_VV(ir->eI);
+    if (bVV) /* to store the initial velocities while computing virial */
+    {
+        snew(cbuf, top_global->natoms);
+    }
+    /* all the iteratative cases - only if there are constraints */
+    bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
+    gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
+                                          false in this step.  The correct value, true or false,
+                                          is set at each step, as it depends on the frequency of temperature
+                                          and pressure control.*/
+    bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
+
+    if (bRerunMD)
+    {
+        /* Since we don't know if the frames read are related in any way,
+         * rebuild the neighborlist at every step.
+         */
+        ir->nstlist       = 1;
+        ir->nstcalcenergy = 1;
+        nstglobalcomm     = 1;
+    }
+
+    check_ir_old_tpx_versions(cr, fplog, ir, top_global);
+
+    nstglobalcomm   = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+    bGStatEveryStep = (nstglobalcomm == 1);
+
+    if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
+    {
+        fprintf(fplog,
+                "To reduce the energy communication with nstlist = -1\n"
+                "the neighbor list validity should not be checked at every step,\n"
+                "this means that exact integration is not guaranteed.\n"
+                "The neighbor list validity is checked after:\n"
+                "  <n.list life time> - 2*std.dev.(n.list life time)  steps.\n"
+                "In most cases this will result in exact integration.\n"
+                "This reduces the energy communication by a factor of 2 to 3.\n"
+                "If you want less energy communication, set nstlist > 3.\n\n");
+    }
+
+    if (bRerunMD)
+    {
+        ir->nstxout_compressed = 0;
+    }
+    groups = &top_global->groups;
+
+    /* Initial values */
+    init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+            &(state_global->fep_state), lam0,
+            nrnb, top_global, &upd,
+            nfile, fnm, &outf, &mdebin,
+            force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, Flags, wcycle);
+
+    clear_mat(total_vir);
+    clear_mat(pres);
+    /* Energy terms and groups */
+    snew(enerd, 1);
+    init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+                  enerd);
+    if (DOMAINDECOMP(cr))
+    {
+        f = NULL;
+    }
+    else
+    {
+        snew(f, top_global->natoms);
+    }
+
+    /* Kinetic energy data */
+    snew(ekind, 1);
+    init_ekindata(fplog, top_global, &(ir->opts), ekind);
+    /* needed for iteration of constraints */
+    snew(ekind_save, 1);
+    init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
+    /* Copy the cos acceleration to the groups struct */
+    ekind->cosacc.cos_accel = ir->cos_accel;
+
+    gstat = global_stat_init(ir);
+    debug_gmx();
+
+    /* Check for polarizable models and flexible constraints */
+    shellfc = init_shell_flexcon(fplog,
+                                 top_global, n_flexible_constraints(constr),
+                                 (ir->bContinuation ||
+                                  (DOMAINDECOMP(cr) && !MASTER(cr))) ?
+                                 NULL : state_global->x);
+    if (shellfc && ir->nstcalcenergy != 1)
+    {
+        gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
+    }
+    if (shellfc && DOMAINDECOMP(cr))
+    {
+        gmx_fatal(FARGS, "Shell particles are not implemented with domain decomposition, use a single rank");
+    }
+    if (shellfc && ir->eI == eiNM)
+    {
+        /* Currently shells don't work with Normal Modes */
+        gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+    }
+
+    if (vsite && ir->eI == eiNM)
+    {
+        /* Currently virtual sites don't work with Normal Modes */
+        gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
+    }
+
+    if (DEFORM(*ir))
+    {
+        tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+        set_deform_reference_box(upd,
+                                 deform_init_init_step_tpx,
+                                 deform_init_box_tpx);
+        tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+    }
+
+    {
+        double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+        if ((io > 2000) && MASTER(cr))
+        {
+            fprintf(stderr,
+                    "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+                    io);
+        }
+    }
+
+    if (DOMAINDECOMP(cr))
+    {
+        top = dd_init_local_top(top_global);
+
+        snew(state, 1);
+        dd_init_local_state(cr->dd, state_global, state);
+
+        if (DDMASTER(cr->dd) && ir->nstfout)
+        {
+            snew(f_global, state_global->natoms);
+        }
+    }
+    else
+    {
+        top = gmx_mtop_generate_local_top(top_global, ir);
+
+        forcerec_set_excl_load(fr, top);
+
+        state    = serial_init_local_state(state_global);
+        f_global = f;
+
+        atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+
+        if (vsite)
+        {
+            set_vsite_top(vsite, top, mdatoms, cr);
+        }
+
+        if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+        {
+            graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+        }
+
+        if (shellfc)
+        {
+            make_local_shells(cr, mdatoms, shellfc);
+        }
+
+        setup_bonded_threading(fr, &top->idef);
+    }
+
+    /* Set up interactive MD (IMD) */
+    init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
+             nfile, fnm, oenv, imdport, Flags);
+
+    if (DOMAINDECOMP(cr))
+    {
+        /* Distribute the charge groups over the nodes from the master node */
+        dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+                            state_global, top_global, ir,
+                            state, &f, mdatoms, top, fr,
+                            vsite, shellfc, constr,
+                            nrnb, wcycle, FALSE);
+
+    }
+
+    update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+    if (opt2bSet("-cpi", nfile, fnm))
+    {
+        bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
+    }
+    else
+    {
+        bStateFromCP = FALSE;
+    }
+
+    if (ir->bExpanded)
+    {
+        init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
+    }
+
+    if (MASTER(cr))
+    {
+        if (bStateFromCP)
+        {
+            /* Update mdebin with energy history if appending to output files */
+            if (Flags & MD_APPENDFILES)
+            {
+                restore_energyhistory_from_state(mdebin, &state_global->enerhist);
+            }
+            else
+            {
+                /* We might have read an energy history from checkpoint,
+                 * free the allocated memory and reset the counts.
+                 */
+                done_energyhistory(&state_global->enerhist);
+                init_energyhistory(&state_global->enerhist);
+            }
+        }
+        /* Set the initial energy history in state by updating once */
+        update_energyhistory(&state_global->enerhist, mdebin);
+    }
+
+    /* Initialize constraints */
+    if (constr && !DOMAINDECOMP(cr))
+    {
+        set_constraints(constr, top, ir, mdatoms, cr);
+    }
+
+    if (repl_ex_nst > 0 && MASTER(cr))
+    {
+        repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
+                                        repl_ex_nst, repl_ex_nex, repl_ex_seed);
+    }
+
+    /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
+     * PME tuning is not supported with PME only for LJ and not for Coulomb.
+     */
+    if ((Flags & MD_TUNEPME) &&
+        EEL_PME(fr->eeltype) &&
+        ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+        !bRerunMD)
+    {
+        pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
+        cycles_pmes = 0;
+        if (cr->duty & DUTY_PME)
+        {
+            /* Start tuning right away, as we can't measure the load */
+            bPMETuneRunning = TRUE;
+        }
+        else
+        {
+            /* Separate PME nodes, we can measure the PP/PME load balance */
+            bPMETuneTry = TRUE;
+        }
+    }
+
+    if (!ir->bContinuation && !bRerunMD)
+    {
+        if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+        {
+            /* Set the velocities of frozen particles to zero */
+            for (i = 0; i < mdatoms->homenr; i++)
+            {
+                for (m = 0; m < DIM; m++)
+                {
+                    if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+                    {
+                        state->v[i][m] = 0;
+                    }
+                }
+            }
+        }
+
+        if (constr)
+        {
+            /* Constrain the initial coordinates and velocities */
+            do_constrain_first(fplog, constr, ir, mdatoms, state,
+                               cr, nrnb, fr, top);
+        }
+        if (vsite)
+        {
+            /* Construct the virtual sites for the initial configuration */
+            construct_vsites(vsite, state->x, ir->delta_t, NULL,
+                             top->idef.iparams, top->idef.il,
+                             fr->ePBC, fr->bMolPBC, cr, state->box);
+        }
+    }
+
+    debug_gmx();
+
+    /* set free energy calculation frequency as the minimum
+       greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
+    nstfep = ir->fepvals->nstdhdl;
+    if (ir->bExpanded)
+    {
+        nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl, nstfep);
+    }
+    if (repl_ex_nst > 0)
+    {
+        nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
+    }
+
+    /* I'm assuming we need global communication the first time! MRS */
+    cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
+                  | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
+                  | (bVV ? CGLO_PRESSURE : 0)
+                  | (bVV ? CGLO_CONSTRAINT : 0)
+                  | (bRerunMD ? CGLO_RERUNMD : 0)
+                  | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+
+    bSumEkinhOld = FALSE;
+    compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                    NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+                    constr, NULL, FALSE, state->box,
+                    top_global, &bSumEkinhOld, cglo_flags);
+    if (ir->eI == eiVVAK)
+    {
+        /* a second call to get the half step temperature initialized as well */
+        /* we do the same call as above, but turn the pressure off -- internally to
+           compute_globals, this is recognized as a velocity verlet half-step
+           kinetic energy calculation.  This minimized excess variables, but
+           perhaps loses some logic?*/
+
+        compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                        NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+                        constr, NULL, FALSE, state->box,
+                        top_global, &bSumEkinhOld,
+                        cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
+    }
+
+    /* Calculate the initial half step temperature, and save the ekinh_old */
+    if (!(Flags & MD_STARTFROMCPT))
+    {
+        for (i = 0; (i < ir->opts.ngtc); i++)
+        {
+            copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
+        }
+    }
+    if (ir->eI != eiVV)
+    {
+        enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
+                                     and there is no previous step */
+    }
+
+    /* if using an iterative algorithm, we need to create a working directory for the state. */
+    if (bIterativeCase)
+    {
+        bufstate = init_bufstate(state);
+    }
+
+    /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
+       temperature control */
+    trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
+
+    if (MASTER(cr))
+    {
+        if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
+        {
+            fprintf(fplog,
+                    "RMS relative constraint deviation after constraining: %.2e\n",
+                    constr_rmsd(constr, FALSE));
+        }
+        if (EI_STATE_VELOCITY(ir->eI))
+        {
+            fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
+        }
+        if (bRerunMD)
+        {
+            fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+                    " input trajectory '%s'\n\n",
+                    *(top_global->name), opt2fn("-rerun", nfile, fnm));
+            if (bVerbose)
+            {
+                fprintf(stderr, "Calculated time to finish depends on nsteps from "
+                        "run input file,\nwhich may not correspond to the time "
+                        "needed to process input trajectory.\n\n");
+            }
+        }
+        else
+        {
+            char tbuf[20];
+            fprintf(stderr, "starting mdrun '%s'\n",
+                    *(top_global->name));
+            if (ir->nsteps >= 0)
+            {
+                sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
+            }
+            else
+            {
+                sprintf(tbuf, "%s", "infinite");
+            }
+            if (ir->init_step > 0)
+            {
+                fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+                        gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
+                        gmx_step_str(ir->init_step, sbuf2),
+                        ir->init_step*ir->delta_t);
+            }
+            else
+            {
+                fprintf(stderr, "%s steps, %s ps.\n",
+                        gmx_step_str(ir->nsteps, sbuf), tbuf);
+            }
+        }
+        fprintf(fplog, "\n");
+    }
+
+    walltime_accounting_start(walltime_accounting);
+    wallcycle_start(wcycle, ewcRUN);
+    print_start(fplog, cr, walltime_accounting, "mdrun");
+
+    /* safest point to do file checkpointing is here.  More general point would be immediately before integrator call */
+#ifdef GMX_FAHCORE
+    chkpt_ret = fcCheckPointParallel( cr->nodeid,
+                                      NULL, 0);
+    if (chkpt_ret == 0)
+    {
+        gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
+    }
+#endif
+
+    debug_gmx();
+    /***********************************************************
+     *
+     *             Loop over MD steps
+     *
+     ************************************************************/
+
+    /* if rerunMD then read coordinates and velocities from input trajectory */
+    if (bRerunMD)
+    {
+        if (getenv("GMX_FORCE_UPDATE"))
+        {
+            bForceUpdate = TRUE;
+        }
+
+        rerun_fr.natoms = 0;
+        if (MASTER(cr))
+        {
+            bNotLastFrame = read_first_frame(oenv, &status,
+                                             opt2fn("-rerun", nfile, fnm),
+                                             &rerun_fr, TRX_NEED_X | TRX_READ_V);
+            if (rerun_fr.natoms != top_global->natoms)
+            {
+                gmx_fatal(FARGS,
+                          "Number of atoms in trajectory (%d) does not match the "
+                          "run input file (%d)\n",
+                          rerun_fr.natoms, top_global->natoms);
+            }
+            if (ir->ePBC != epbcNONE)
+            {
+                if (!rerun_fr.bBox)
+                {
+                    gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
+                }
+                if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
+                {
+                    gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
+                }
+            }
+        }
+
+        if (PAR(cr))
+        {
+            rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+        }
+
+        if (ir->ePBC != epbcNONE)
+        {
+            /* Set the shift vectors.
+             * Necessary here when have a static box different from the tpr box.
+             */
+            calc_shifts(rerun_fr.box, fr->shift_vec);
+        }
+    }
+
+    /* loop over MD steps or if rerunMD to end of input trajectory */
+    bFirstStep = TRUE;
+    /* Skip the first Nose-Hoover integration when we get the state from tpx */
+    bStateFromTPX    = !bStateFromCP;
+    bInitStep        = bFirstStep && (bStateFromTPX || bVV);
+    bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
+    bLastStep        = FALSE;
+    bSumEkinhOld     = FALSE;
+    bDoReplEx        = FALSE;
+    bExchanged       = FALSE;
+    bNeedRepartition = FALSE;
+
+    init_global_signals(&gs, cr, ir, repl_ex_nst);
+
+    step     = ir->init_step;
+    step_rel = 0;
+
+    if (ir->nstlist == -1)
+    {
+        init_nlistheuristics(&nlh, bGStatEveryStep, step);
+    }
+
+    if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+    {
+        /* check how many steps are left in other sims */
+        multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+    }
+
+
+    /* and stop now if we should */
+    bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
+                 ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+    while (!bLastStep || (bRerunMD && bNotLastFrame))
+    {
+
+        wallcycle_start(wcycle, ewcSTEP);
+
+        if (bRerunMD)
+        {
+            if (rerun_fr.bStep)
+            {
+                step     = rerun_fr.step;
+                step_rel = step - ir->init_step;
+            }
+            if (rerun_fr.bTime)
+            {
+                t = rerun_fr.time;
+            }
+            else
+            {
+                t = step;
+            }
+        }
+        else
+        {
+            bLastStep = (step_rel == ir->nsteps);
+            t         = t0 + step*ir->delta_t;
+        }
+
+        if (ir->efep != efepNO || ir->bSimTemp)
+        {
+            /* find and set the current lambdas.  If rerunning, we either read in a state, or a lambda value,
+               requiring different logic. */
+
+            set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
+            bDoDHDL      = do_per_step(step, ir->fepvals->nstdhdl);
+            bDoFEP       = (do_per_step(step, nstfep) && (ir->efep != efepNO));
+            bDoExpanded  = (do_per_step(step, ir->expandedvals->nstexpanded)
+                            && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
+        }
+
+        bDoReplEx = ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+                     do_per_step(step, repl_ex_nst));
+
+        if (bSimAnn)
+        {
+            update_annealing_target_temp(&(ir->opts), t);
+        }
+
+        if (bRerunMD)
+        {
+            if (!DOMAINDECOMP(cr) || MASTER(cr))
+            {
+                for (i = 0; i < state_global->natoms; i++)
+                {
+                    copy_rvec(rerun_fr.x[i], state_global->x[i]);
+                }
+                if (rerun_fr.bV)
+                {
+                    for (i = 0; i < state_global->natoms; i++)
+                    {
+                        copy_rvec(rerun_fr.v[i], state_global->v[i]);
+                    }
+                }
+                else
+                {
+                    for (i = 0; i < state_global->natoms; i++)
+                    {
+                        clear_rvec(state_global->v[i]);
+                    }
+                    if (bRerunWarnNoV)
+                    {
+                        fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
+                                "         Ekin, temperature and pressure are incorrect,\n"
+                                "         the virial will be incorrect when constraints are present.\n"
+                                "\n");
+                        bRerunWarnNoV = FALSE;
+                    }
+                }
+            }
+            copy_mat(rerun_fr.box, state_global->box);
+            copy_mat(state_global->box, state->box);
+
+            if (vsite && (Flags & MD_RERUN_VSITE))
+            {
+                if (DOMAINDECOMP(cr))
+                {
+                    gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, use a single rank");
+                }
+                if (graph)
+                {
+                    /* Following is necessary because the graph may get out of sync
+                     * with the coordinates if we only have every N'th coordinate set
+                     */
+                    mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+                    shift_self(graph, state->box, state->x);
+                }
+                construct_vsites(vsite, state->x, ir->delta_t, state->v,
+                                 top->idef.iparams, top->idef.il,
+                                 fr->ePBC, fr->bMolPBC, cr, state->box);
+                if (graph)
+                {
+                    unshift_self(graph, state->box, state->x);
+                }
+            }
+        }
+
+        /* Stop Center of Mass motion */
+        bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+
+        if (bRerunMD)
+        {
+            /* for rerun MD always do Neighbour Searching */
+            bNS      = (bFirstStep || ir->nstlist != 0);
+            bNStList = bNS;
+        }
+        else
+        {
+            /* Determine whether or not to do Neighbour Searching and LR */
+            bNStList = (ir->nstlist > 0  && step % ir->nstlist == 0);
+
+            bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
+                   (ir->nstlist == -1 && nlh.nabnsb > 0));
+
+            if (bNS && ir->nstlist == -1)
+            {
+                set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
+            }
+        }
+
+        /* check whether we should stop because another simulation has
+           stopped. */
+        if (MULTISIM(cr))
+        {
+            if ( (multisim_nsteps >= 0) &&  (step_rel >= multisim_nsteps)  &&
+                 (multisim_nsteps != ir->nsteps) )
+            {
+                if (bNS)
+                {
+                    if (MASTER(cr))
+                    {
+                        fprintf(stderr,
+                                "Stopping simulation %d because another one has finished\n",
+                                cr->ms->sim);
+                    }
+                    bLastStep         = TRUE;
+                    gs.sig[eglsCHKPT] = 1;
+                }
+            }
+        }
+
+        /* < 0 means stop at next step, > 0 means stop at next NS step */
+        if ( (gs.set[eglsSTOPCOND] < 0) ||
+             ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+        {
+            bLastStep = TRUE;
+        }
+
+        /* Determine whether or not to update the Born radii if doing GB */
+        bBornRadii = bFirstStep;
+        if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
+        {
+            bBornRadii = TRUE;
+        }
+
+        do_log     = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+        do_verbose = bVerbose &&
+            (step % stepout == 0 || bFirstStep || bLastStep);
+
+        if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
+        {
+            if (bRerunMD)
+            {
+                bMasterState = TRUE;
+            }
+            else
+            {
+                bMasterState = FALSE;
+                /* Correct the new box if it is too skewed */
+                if (DYNAMIC_BOX(*ir))
+                {
+                    if (correct_box(fplog, step, state->box, graph))
+                    {
+                        bMasterState = TRUE;
+                    }
+                }
+                if (DOMAINDECOMP(cr) && bMasterState)
+                {
+                    dd_collect_state(cr->dd, state, state_global);
+                }
+            }
+
+            if (DOMAINDECOMP(cr))
+            {
+                /* Repartition the domain decomposition */
+                wallcycle_start(wcycle, ewcDOMDEC);
+                dd_partition_system(fplog, step, cr,
+                                    bMasterState, nstglobalcomm,
+                                    state_global, top_global, ir,
+                                    state, &f, mdatoms, top, fr,
+                                    vsite, shellfc, constr,
+                                    nrnb, wcycle,
+                                    do_verbose && !bPMETuneRunning);
+                wallcycle_stop(wcycle, ewcDOMDEC);
+                /* If using an iterative integrator, reallocate space to match the decomposition */
+            }
+        }
+
+        if (MASTER(cr) && do_log)
+        {
+            print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
+        }
+
+        if (ir->efep != efepNO)
+        {
+            update_mdatoms(mdatoms, state->lambda[efptMASS]);
+        }
+
+        if ((bRerunMD && rerun_fr.bV) || bExchanged)
+        {
+
+            /* We need the kinetic energy at minus the half step for determining
+             * the full step kinetic energy and possibly for T-coupling.*/
+            /* This may not be quite working correctly yet . . . . */
+            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                            wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+                            constr, NULL, FALSE, state->box,
+                            top_global, &bSumEkinhOld,
+                            CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+        }
+        clear_mat(force_vir);
+
+        /* We write a checkpoint at this MD step when:
+         * either at an NS step when we signalled through gs,
+         * or at the last step (but not when we do not want confout),
+         * but never at the first step or with rerun.
+         */
+        bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+                 (bLastStep && (Flags & MD_CONFOUT))) &&
+                step > ir->init_step && !bRerunMD);
+        if (bCPT)
+        {
+            gs.set[eglsCHKPT] = 0;
+        }
+
+        /* Determine the energy and pressure:
+         * at nstcalcenergy steps and at energy output steps (set below).
+         */
+        if (EI_VV(ir->eI) && (!bInitStep))
+        {
+            /* for vv, the first half of the integration actually corresponds
+               to the previous step.  bCalcEner is only required to be evaluated on the 'next' step,
+               but the virial needs to be calculated on both the current step and the 'next' step. Future
+               reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
+
+            bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
+            bCalcVir  = bCalcEner ||
+                (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
+        }
+        else
+        {
+            bCalcEner = do_per_step(step, ir->nstcalcenergy);
+            bCalcVir  = bCalcEner ||
+                (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+        }
+
+        /* Do we need global communication ? */
+        bGStat = (bCalcVir || bCalcEner || bStopCM ||
+                  do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
+                  (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+
+        do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
+
+        if (do_ene || do_log || bDoReplEx)
+        {
+            bCalcVir  = TRUE;
+            bCalcEner = TRUE;
+            bGStat    = TRUE;
+        }
+
+        /* these CGLO_ options remain the same throughout the iteration */
+        cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
+                      (bGStat ? CGLO_GSTAT : 0)
+                      );
+
+        force_flags = (GMX_FORCE_STATECHANGED |
+                       ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+                       GMX_FORCE_ALLFORCES |
+                       GMX_FORCE_SEPLRF |
+                       (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
+                       (bCalcEner ? GMX_FORCE_ENERGY : 0) |
+                       (bDoFEP ? GMX_FORCE_DHDL : 0)
+                       );
+
+        if (fr->bTwinRange)
+        {
+            if (do_per_step(step, ir->nstcalclr))
+            {
+                force_flags |= GMX_FORCE_DO_LR;
+            }
+        }
+
+        if (shellfc)
+        {
+            /* Now is the time to relax the shells */
+            count = relax_shell_flexcon(fplog, cr, bVerbose, step,
+                                        ir, bNS, force_flags,
+                                        top,
+                                        constr, enerd, fcd,
+                                        state, f, force_vir, mdatoms,
+                                        nrnb, wcycle, graph, groups,
+                                        shellfc, fr, bBornRadii, t, mu_tot,
+                                        &bConverged, vsite,
+                                        mdoutf_get_fp_field(outf));
+            tcount += count;
+
+            if (bConverged)
+            {
+                nconverged++;
+            }
+        }
+        else
+        {
+            /* The coordinates (x) are shifted (to get whole molecules)
+             * in do_force.
+             * This is parallellized as well, and does communication too.
+             * Check comments in sim_util.c
+             */
+            do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
+                     state->box, state->x, &state->hist,
+                     f, force_vir, mdatoms, enerd, fcd,
+                     state->lambda, graph,
+                     fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
+                     (bNS ? GMX_FORCE_NS : 0) | force_flags);
+        }
+
+        if (bVV && !bStartingFromCpt && !bRerunMD)
+        /*  ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+        {
+            wallcycle_start(wcycle, ewcUPDATE);
+            if (ir->eI == eiVV && bInitStep)
+            {
+                /* if using velocity verlet with full time step Ekin,
+                 * take the first half step only to compute the
+                 * virial for the first step. From there,
+                 * revert back to the initial coordinates
+                 * so that the input is actually the initial step.
+                 */
+                copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+            }
+            else
+            {
+                /* this is for NHC in the Ekin(t+dt/2) version of vv */
+                trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
+            }
+
+            /* If we are using twin-range interactions where the long-range component
+             * is only evaluated every nstcalclr>1 steps, we should do a special update
+             * step to combine the long-range forces on these steps.
+             * For nstcalclr=1 this is not done, since the forces would have been added
+             * directly to the short-range forces already.
+             *
+             * TODO Remove various aspects of VV+twin-range in master
+             * branch, because VV integrators did not ever support
+             * twin-range multiple time stepping with constraints.
+             */
+            bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+            update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
+                          f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
+                          ekind, M, upd, bInitStep, etrtVELOCITY1,
+                          cr, nrnb, constr, &top->idef);
+
+            if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
+            {
+                gmx_iterate_init(&iterate, TRUE);
+            }
+            /* for iterations, we save these vectors, as we will be self-consistently iterating
+               the calculations */
+
+            /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
+
+            /* save the state */
+            if (iterate.bIterationActive)
+            {
+                copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+            }
+
+            bFirstIterate = TRUE;
+            while (bFirstIterate || iterate.bIterationActive)
+            {
+                if (iterate.bIterationActive)
+                {
+                    copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+                    if (bFirstIterate && bTrotter)
+                    {
+                        /* The first time through, we need a decent first estimate
+                           of veta(t+dt) to compute the constraints.  Do
+                           this by computing the box volume part of the
+                           trotter integration at this time. Nothing else
+                           should be changed by this routine here.  If
+                           !(first time), we start with the previous value
+                           of veta.  */
+
+                        veta_save = state->veta;
+                        trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
+                        vetanew     = state->veta;
+                        state->veta = veta_save;
+                    }
+                }
+
+                bOK = TRUE;
+                if (!bRerunMD || rerun_fr.bV || bForceUpdate)     /* Why is rerun_fr.bV here?  Unclear. */
+                {
+                    wallcycle_stop(wcycle, ewcUPDATE);
+                    update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+                                       state, fr->bMolPBC, graph, f,
+                                       &top->idef, shake_vir,
+                                       cr, nrnb, wcycle, upd, constr,
+                                       TRUE, bCalcVir, vetanew);
+                    wallcycle_start(wcycle, ewcUPDATE);
+
+                    if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+                    {
+                        /* Correct the virial for multiple time stepping */
+                        m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+                    }
+
+                    if (!bOK)
+                    {
+                        gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+                    }
+
+                }
+                else if (graph)
+                {
+                    /* Need to unshift here if a do_force has been
+                       called in the previous step */
+                    unshift_self(graph, state->box, state->x);
+                }
+
+                /* if VV, compute the pressure and constraints */
+                /* For VV2, we strictly only need this if using pressure
+                 * control, but we really would like to have accurate pressures
+                 * printed out.
+                 * Think about ways around this in the future?
+                 * For now, keep this choice in comments.
+                 */
+                /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
+                /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
+                bPres = TRUE;
+                bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
+                if (bCalcEner && ir->eI == eiVVAK)  /*MRS:  7/9/2010 -- this still doesn't fix it?*/
+                {
+                    bSumEkinhOld = TRUE;
+                }
+                /* for vv, the first half of the integration actually corresponds to the previous step.
+                   So we need information from the last step in the first half of the integration */
+                if (bGStat || do_per_step(step-1, nstglobalcomm))
+                {
+                    wallcycle_stop(wcycle, ewcUPDATE);
+                    compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                                    wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+                                    constr, NULL, FALSE, state->box,
+                                    top_global, &bSumEkinhOld,
+                                    cglo_flags
+                                    | CGLO_ENERGY
+                                    | (bTemp ? CGLO_TEMPERATURE : 0)
+                                    | (bPres ? CGLO_PRESSURE : 0)
+                                    | (bPres ? CGLO_CONSTRAINT : 0)
+                                    | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
+                                    | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+                                    | CGLO_SCALEEKIN
+                                    );
+                    /* explanation of above:
+                       a) We compute Ekin at the full time step
+                       if 1) we are using the AveVel Ekin, and it's not the
+                       initial step, or 2) if we are using AveEkin, but need the full
+                       time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+                       b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+                       EkinAveVel because it's needed for the pressure */
+                    wallcycle_start(wcycle, ewcUPDATE);
+                }
+                /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+                if (!bInitStep)
+                {
+                    if (bTrotter)
+                    {
+                        m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+                        trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
+                    }
+                    else
+                    {
+                        if (bExchanged)
+                        {
+                            wallcycle_stop(wcycle, ewcUPDATE);
+                            /* We need the kinetic energy at minus the half step for determining
+                             * the full step kinetic energy and possibly for T-coupling.*/
+                            /* This may not be quite working correctly yet . . . . */
+                            compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                                            wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+                                            constr, NULL, FALSE, state->box,
+                                            top_global, &bSumEkinhOld,
+                                            CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+                            wallcycle_start(wcycle, ewcUPDATE);
+                        }
+                    }
+                }
+
+                if (iterate.bIterationActive &&
+                    done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+                                   state->veta, &vetanew))
+                {
+                    break;
+                }
+                bFirstIterate = FALSE;
+            }
+
+            if (bTrotter && !bInitStep)
+            {
+                copy_mat(shake_vir, state->svir_prev);
+                copy_mat(force_vir, state->fvir_prev);
+                if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
+                {
+                    /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+                    enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE);
+                    enerd->term[F_EKIN] = trace(ekind->ekin);
+                }
+            }
+            /* if it's the initial step, we performed this first step just to get the constraint virial */
+            if (bInitStep && ir->eI == eiVV)
+            {
+                copy_rvecn(cbuf, state->v, 0, state->natoms);
+            }
+            wallcycle_stop(wcycle, ewcUPDATE);
+        }
+
+        /* MRS -- now done iterating -- compute the conserved quantity */
+        if (bVV)
+        {
+            saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+            if (ir->eI == eiVV)
+            {
+                last_ekin = enerd->term[F_EKIN];
+            }
+            if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
+            {
+                saved_conserved_quantity -= enerd->term[F_DISPCORR];
+            }
+            /* sum up the foreign energy and dhdl terms for vv.  currently done every step so that dhdl is correct in the .edr */
+            if (!bRerunMD)
+            {
+                sum_dhdl(enerd, state->lambda, ir->fepvals);
+            }
+        }
+
+        /* ########  END FIRST UPDATE STEP  ############## */
+        /* ########  If doing VV, we now have v(dt) ###### */
+        if (bDoExpanded)
+        {
+            /* perform extended ensemble sampling in lambda - we don't
+               actually move to the new state before outputting
+               statistics, but if performing simulated tempering, we
+               do update the velocities and the tau_t. */
+
+            lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, state->v, mdatoms);
+            /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
+            copy_df_history(&state_global->dfhist, &state->dfhist);
+        }
+
+        /* Now we have the energies and forces corresponding to the
+         * coordinates at time t. We must output all of this before
+         * the update.
+         */
+        do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
+                                 ir, state, state_global, top_global, fr,
+                                 outf, mdebin, ekind, f, f_global,
+                                 &nchkpt,
+                                 bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
+                                 bSumEkinhOld);
+        /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
+        bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
+
+        /* kludge -- virial is lost with restart for NPT control. Must restart */
+        if (bStartingFromCpt && bVV)
+        {
+            copy_mat(state->svir_prev, shake_vir);
+            copy_mat(state->fvir_prev, force_vir);
+        }
+
+        elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
+
+        /* Check whether everything is still allright */
+        if (((int)gmx_get_stop_condition() > handled_stop_condition)
+#ifdef GMX_THREAD_MPI
+            && MASTER(cr)
+#endif
+            )
+        {
+            /* this is just make gs.sig compatible with the hack
+               of sending signals around by MPI_Reduce with together with
+               other floats */
+            if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
+            {
+                gs.sig[eglsSTOPCOND] = 1;
+            }
+            if (gmx_get_stop_condition() == gmx_stop_cond_next)
+            {
+                gs.sig[eglsSTOPCOND] = -1;
+            }
+            /* < 0 means stop at next step, > 0 means stop at next NS step */
+            if (fplog)
+            {
+                fprintf(fplog,
+                        "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+                        gmx_get_signal_name(),
+                        gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+                fflush(fplog);
+            }
+            fprintf(stderr,
+                    "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+                    gmx_get_signal_name(),
+                    gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+            fflush(stderr);
+            handled_stop_condition = (int)gmx_get_stop_condition();
+        }
+        else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
+                 (max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
+                 gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+        {
+            /* Signal to terminate the run */
+            gs.sig[eglsSTOPCOND] = 1;
+            if (fplog)
+            {
+                fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+            }
+            fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+        }
+
+        if (bResetCountersHalfMaxH && MASTER(cr) &&
+            elapsed_time > max_hours*60.0*60.0*0.495)
+        {
+            gs.sig[eglsRESETCOUNTERS] = 1;
+        }
+
+        if (ir->nstlist == -1 && !bRerunMD)
+        {
+            /* When bGStatEveryStep=FALSE, global_stat is only called
+             * when we check the atom displacements, not at NS steps.
+             * This means that also the bonded interaction count check is not
+             * performed immediately after NS. Therefore a few MD steps could
+             * be performed with missing interactions.
+             * But wrong energies are never written to file,
+             * since energies are only written after global_stat
+             * has been called.
+             */
+            if (step >= nlh.step_nscheck)
+            {
+                nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
+                                                     nlh.scale_tot, state->x);
+            }
+            else
+            {
+                /* This is not necessarily true,
+                 * but step_nscheck is determined quite conservatively.
+                 */
+                nlh.nabnsb = 0;
+            }
+        }
+
+        /* In parallel we only have to check for checkpointing in steps
+         * where we do global communication,
+         *  otherwise the other nodes don't know.
+         */
+        if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
+                           cpt_period >= 0 &&
+                           (cpt_period == 0 ||
+                            elapsed_time >= nchkpt*cpt_period*60.0)) &&
+            gs.set[eglsCHKPT] == 0)
+        {
+            gs.sig[eglsCHKPT] = 1;
+        }
+
+        /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
+        if (EI_VV(ir->eI))
+        {
+            if (!bInitStep)
+            {
+                update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
+            }
+            if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+            {
+                gmx_bool bIfRandomize;
+                bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
+                /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+                if (constr && bIfRandomize)
+                {
+                    update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+                                       state, fr->bMolPBC, graph, f,
+                                       &top->idef, tmp_vir,
+                                       cr, nrnb, wcycle, upd, constr,
+                                       TRUE, bCalcVir, vetanew);
+                }
+            }
+        }
+
+        if (bIterativeCase && do_per_step(step, ir->nstpcouple))
+        {
+            gmx_iterate_init(&iterate, TRUE);
+            /* for iterations, we save these vectors, as we will be redoing the calculations */
+            copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+        }
+
+        bFirstIterate = TRUE;
+        while (bFirstIterate || iterate.bIterationActive)
+        {
+            /* We now restore these vectors to redo the calculation with improved extended variables */
+            if (iterate.bIterationActive)
+            {
+                copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+            }
+
+            /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
+               so scroll down for that logic */
+
+            /* #########   START SECOND UPDATE STEP ################# */
+            /* Box is changed in update() when we do pressure coupling,
+             * but we should still use the old box for energy corrections and when
+             * writing it to the energy file, so it matches the trajectory files for
+             * the same timestep above. Make a copy in a separate array.
+             */
+            copy_mat(state->box, lastbox);
+
+            bOK         = TRUE;
+            dvdl_constr = 0;
+
+            if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+            {
+                wallcycle_start(wcycle, ewcUPDATE);
+                /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
+                if (bTrotter)
+                {
+                    if (iterate.bIterationActive)
+                    {
+                        if (bFirstIterate)
+                        {
+                            scalevir = 1;
+                        }
+                        else
+                        {
+                            /* we use a new value of scalevir to converge the iterations faster */
+                            scalevir = tracevir/trace(shake_vir);
+                        }
+                        msmul(shake_vir, scalevir, shake_vir);
+                        m_add(force_vir, shake_vir, total_vir);
+                        clear_mat(shake_vir);
+                    }
+                    trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
+                    /* We can only do Berendsen coupling after we have summed
+                     * the kinetic energy or virial. Since the happens
+                     * in global_state after update, we should only do it at
+                     * step % nstlist = 1 with bGStatEveryStep=FALSE.
+                     */
+                }
+                else
+                {
+                    update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
+                    update_pcouple(fplog, step, ir, state, pcoupl_mu, M, bInitStep);
+                }
+
+                if (bVV)
+                {
+                    bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+                    /* velocity half-step update */
+                    update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+                                  bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
+                                  ekind, M, upd, FALSE, etrtVELOCITY2,
+                                  cr, nrnb, constr, &top->idef);
+                }
+
+                /* Above, initialize just copies ekinh into ekin,
+                 * it doesn't copy position (for VV),
+                 * and entire integrator for MD.
+                 */
+
+                if (ir->eI == eiVVAK)
+                {
+                    copy_rvecn(state->x, cbuf, 0, state->natoms);
+                }
+                bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+                update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+                              bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
+                              ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+                wallcycle_stop(wcycle, ewcUPDATE);
+
+                update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+                                   fr->bMolPBC, graph, f,
+                                   &top->idef, shake_vir,
+                                   cr, nrnb, wcycle, upd, constr,
+                                   FALSE, bCalcVir, state->veta);
+
+                if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+                {
+                    /* Correct the virial for multiple time stepping */
+                    m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+                }
+
+                if (ir->eI == eiVVAK)
+                {
+                    /* erase F_EKIN and F_TEMP here? */
+                    /* just compute the kinetic energy at the half step to perform a trotter step */
+                    compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                                    wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+                                    constr, NULL, FALSE, lastbox,
+                                    top_global, &bSumEkinhOld,
+                                    cglo_flags | CGLO_TEMPERATURE
+                                    );
+                    wallcycle_start(wcycle, ewcUPDATE);
+                    trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
+                    /* now we know the scaling, we can compute the positions again again */
+                    copy_rvecn(cbuf, state->x, 0, state->natoms);
+
+                    bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+                    update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+                                  bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
+                                  ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+                    wallcycle_stop(wcycle, ewcUPDATE);
+
+                    /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+                    /* are the small terms in the shake_vir here due
+                     * to numerical errors, or are they important
+                     * physically? I'm thinking they are just errors, but not completely sure.
+                     * For now, will call without actually constraining, constr=NULL*/
+                    update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+                                       state, fr->bMolPBC, graph, f,
+                                       &top->idef, tmp_vir,
+                                       cr, nrnb, wcycle, upd, NULL,
+                                       FALSE, bCalcVir,
+                                       state->veta);
+                }
+                if (!bOK)
+                {
+                    gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+                }
+
+                if (fr->bSepDVDL && fplog && do_log)
+                {
+                    gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
+                }
+                if (bVV)
+                {
+                    /* this factor or 2 correction is necessary
+                       because half of the constraint force is removed
+                       in the vv step, so we have to double it.  See
+                       the Redmine issue #1255.  It is not yet clear
+                       if the factor of 2 is exact, or just a very
+                       good approximation, and this will be
+                       investigated.  The next step is to see if this
+                       can be done adding a dhdl contribution from the
+                       rattle step, but this is somewhat more
+                       complicated with the current code. Will be
+                       investigated, hopefully for 4.6.3. However,
+                       this current solution is much better than
+                       having it completely wrong.
+                     */
+                    enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
+                }
+                else
+                {
+                    enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+                }
+            }
+            else if (graph)
+            {
+                /* Need to unshift here */
+                unshift_self(graph, state->box, state->x);
+            }
+
+            if (vsite != NULL)
+            {
+                wallcycle_start(wcycle, ewcVSITECONSTR);
+                if (graph != NULL)
+                {
+                    shift_self(graph, state->box, state->x);
+                }
+                construct_vsites(vsite, state->x, ir->delta_t, state->v,
+                                 top->idef.iparams, top->idef.il,
+                                 fr->ePBC, fr->bMolPBC, cr, state->box);
+
+                if (graph != NULL)
+                {
+                    unshift_self(graph, state->box, state->x);
+                }
+                wallcycle_stop(wcycle, ewcVSITECONSTR);
+            }
+
+            /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints  ############ */
+            /* With Leap-Frog we can skip compute_globals at
+             * non-communication steps, but we need to calculate
+             * the kinetic energy one step before communication.
+             */
+            if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
+            {
+                if (ir->nstlist == -1 && bFirstIterate)
+                {
+                    gs.sig[eglsNABNSB] = nlh.nabnsb;
+                }
+                compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+                                wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+                                constr,
+                                bFirstIterate ? &gs : NULL,
+                                (step_rel % gs.nstms == 0) &&
+                                (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
+                                lastbox,
+                                top_global, &bSumEkinhOld,
+                                cglo_flags
+                                | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+                                | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+                                | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+                                | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+                                | (iterate.bIterationActive ? CGLO_ITERATE : 0)
+                                | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+                                | CGLO_CONSTRAINT
+                                );
+                if (ir->nstlist == -1 && bFirstIterate)
+                {
+                    nlh.nabnsb         = gs.set[eglsNABNSB];
+                    gs.set[eglsNABNSB] = 0;
+                }
+            }
+            /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+            /* #############  END CALC EKIN AND PRESSURE ################# */
+
+            /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+               the virial that should probably be addressed eventually. state->veta has better properies,
+               but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+               generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
+
+            if (iterate.bIterationActive &&
+                done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+                               trace(shake_vir), &tracevir))
+            {
+                break;
+            }
+            bFirstIterate = FALSE;
+        }
+
+        if (!bVV || bRerunMD)
+        {
+            /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+            sum_dhdl(enerd, state->lambda, ir->fepvals);
+        }
+        update_box(fplog, step, ir, mdatoms, state, f,
+                   ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, upd);
+
+        /* ################# END UPDATE STEP 2 ################# */
+        /* #### We now have r(t+dt) and v(t+dt/2)  ############# */
+
+        /* The coordinates (x) were unshifted in update */
+        if (!bGStat)
+        {
+            /* We will not sum ekinh_old,
+             * so signal that we still have to do it.
+             */
+            bSumEkinhOld = TRUE;
+        }
+
+        /* #########  BEGIN PREPARING EDR OUTPUT  ###########  */
+
+        /* use the directly determined last velocity, not actually the averaged half steps */
+        if (bTrotter && ir->eI == eiVV)
+        {
+            enerd->term[F_EKIN] = last_ekin;
+        }
+        enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+        if (bVV)
+        {
+            enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+        }
+        else
+        {
+            enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+        }
+        /* #########  END PREPARING EDR OUTPUT  ###########  */
+
+        /* Output stuff */
+        if (MASTER(cr))
+        {
+            gmx_bool do_dr, do_or;
+
+            if (fplog && do_log && bDoExpanded)
+            {
+                /* only needed if doing expanded ensemble */
+                PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+                                          &state_global->dfhist, state->fep_state, ir->nstlog, step);
+            }
+            if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+            {
+                if (bCalcEner)
+                {
+                    upd_mdebin(mdebin, bDoDHDL, TRUE,
+                               t, mdatoms->tmass, enerd, state,
+                               ir->fepvals, ir->expandedvals, lastbox,
+                               shake_vir, force_vir, total_vir, pres,
+                               ekind, mu_tot, constr);
+                }
+                else
+                {
+                    upd_mdebin_step(mdebin);
+                }
+
+                do_dr  = do_per_step(step, ir->nstdisreout);
+                do_or  = do_per_step(step, ir->nstorireout);
+
+                print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+                           step, t,
+                           eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
+            }
+            if (ir->ePull != epullNO)
+            {
+                pull_print_output(ir->pull, step, t);
+            }
+
+            if (do_per_step(step, ir->nstlog))
+            {
+                if (fflush(fplog) != 0)
+                {
+                    gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+                }
+            }
+        }
+        if (bDoExpanded)
+        {
+            /* Have to do this part _after_ outputting the logfile and the edr file */
+            /* Gets written into the state at the beginning of next loop*/
+            state->fep_state = lamnew;
+        }
+        /* Print the remaining wall clock time for the run */
+        if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
+        {
+            if (shellfc)
+            {
+                fprintf(stderr, "\n");
+            }
+            print_time(stderr, walltime_accounting, step, ir, cr);
+        }
+
+        /* Ion/water position swapping.
+         * Not done in last step since trajectory writing happens before this call
+         * in the MD loop and exchanges would be lost anyway. */
+        bNeedRepartition = FALSE;
+        if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
+            do_per_step(step, ir->swap->nstswap))
+        {
+            bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
+                                             bRerunMD ? rerun_fr.x   : state->x,
+                                             bRerunMD ? rerun_fr.box : state->box,
+                                             top_global, MASTER(cr) && bVerbose, bRerunMD);
+
+            if (bNeedRepartition && DOMAINDECOMP(cr))
+            {
+                dd_collect_state(cr->dd, state, state_global);
+            }
+        }
+
+        /* Replica exchange */
+        bExchanged = FALSE;
+        if (bDoReplEx)
+        {
+            bExchanged = replica_exchange(fplog, cr, repl_ex,
+                                          state_global, enerd,
+                                          state, step, t);
+        }
+
+        if ( (bExchanged || bNeedRepartition) && DOMAINDECOMP(cr) )
+        {
+            dd_partition_system(fplog, step, cr, TRUE, 1,
+                                state_global, top_global, ir,
+                                state, &f, mdatoms, top, fr,
+                                vsite, shellfc, constr,
+                                nrnb, wcycle, FALSE);
+        }
+
+        bFirstStep       = FALSE;
+        bInitStep        = FALSE;
+        bStartingFromCpt = FALSE;
+
+        /* #######  SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
+        /* With all integrators, except VV, we need to retain the pressure
+         * at the current step for coupling at the next step.
+         */
+        if ((state->flags & (1<<estPRES_PREV)) &&
+            (bGStatEveryStep ||
+             (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
+        {
+            /* Store the pressure in t_state for pressure coupling
+             * at the next MD step.
+             */
+            copy_mat(pres, state->pres_prev);
+        }
+
+        /* #######  END SET VARIABLES FOR NEXT ITERATION ###### */
+
+        if ( (membed != NULL) && (!bLastStep) )
+        {
+            rescale_membed(step_rel, membed, state_global->x);
+        }
+
+        if (bRerunMD)
+        {
+            if (MASTER(cr))
+            {
+                /* read next frame from input trajectory */
+                bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
+            }
+
+            if (PAR(cr))
+            {
+                rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+            }
+        }
+
+        if (!bRerunMD || !rerun_fr.bStep)
+        {
+            /* increase the MD step number */
+            step++;
+            step_rel++;
+        }
+
+        cycles = wallcycle_stop(wcycle, ewcSTEP);
+        if (DOMAINDECOMP(cr) && wcycle)
+        {
+            dd_cycles_add(cr->dd, cycles, ddCyclStep);
+        }
+
+        if (bPMETuneRunning || bPMETuneTry)
+        {
+            /* PME grid + cut-off optimization with GPUs or PME nodes */
+
+            /* Count the total cycles over the last steps */
+            cycles_pmes += cycles;
+
+            /* We can only switch cut-off at NS steps */
+            if (step % ir->nstlist == 0)
+            {
+                /* PME grid + cut-off optimization with GPUs or PME nodes */
+                if (bPMETuneTry)
+                {
+                    if (DDMASTER(cr->dd))
+                    {
+                        /* PME node load is too high, start tuning */
+                        bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
+                    }
+                    dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
+
+                    if (bPMETuneRunning &&
+                        fr->nbv->bUseGPU && DOMAINDECOMP(cr) &&
+                        !(cr->duty & DUTY_PME))
+                    {
+                        /* Lock DLB=auto to off (does nothing when DLB=yes/no).
+                         * With GPUs + separate PME ranks, we don't want DLB.
+                         * This could happen when we scan coarse grids and
+                         * it would then never be turned off again.
+                         * This would hurt performance at the final, optimal
+                         * grid spacing, where DLB almost never helps.
+                         * Also, DLB can limit the cut-off for PME tuning.
+                         */
+                        dd_dlb_set_lock(cr->dd, TRUE);
+                    }
+
+                    if (bPMETuneRunning || step_rel > ir->nstlist*50)
+                    {
+                        bPMETuneTry     = FALSE;
+                    }
+                }
+                if (bPMETuneRunning)
+                {
+                    /* init_step might not be a multiple of nstlist,
+                     * but the first cycle is always skipped anyhow.
+                     */
+                    bPMETuneRunning =
+                        pme_load_balance(pme_loadbal, cr,
+                                         (bVerbose && MASTER(cr)) ? stderr : NULL,
+                                         fplog,
+                                         ir, state, cycles_pmes,
+                                         fr->ic, fr->nbv, &fr->pmedata,
+                                         step);
+
+                    /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
+                    fr->ewaldcoeff_q  = fr->ic->ewaldcoeff_q;
+                    fr->ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
+                    fr->rlist         = fr->ic->rlist;
+                    fr->rlistlong     = fr->ic->rlistlong;
+                    fr->rcoulomb      = fr->ic->rcoulomb;
+                    fr->rvdw          = fr->ic->rvdw;
+
+                    if (ir->eDispCorr != edispcNO)
+                    {
+                        calc_enervirdiff(NULL, ir->eDispCorr, fr);
+                    }
+
+                    if (!bPMETuneRunning &&
+                        DOMAINDECOMP(cr) &&
+                        dd_dlb_is_locked(cr->dd))
+                    {
+                        /* Unlock the DLB=auto, DLB is allowed to activate
+                         * (but we don't expect it to activate in most cases).
+                         */
+                        dd_dlb_set_lock(cr->dd, FALSE);
+                    }
+                }
+                cycles_pmes = 0;
+            }
+        }
+
+        if (step_rel == wcycle_get_reset_counters(wcycle) ||
+            gs.set[eglsRESETCOUNTERS] != 0)
+        {
+            /* Reset all the counters related to performance over the run */
+            reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
+                               fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+            wcycle_set_reset_counters(wcycle, -1);
+            if (!(cr->duty & DUTY_PME))
+            {
+                /* Tell our PME node to reset its counters */
+                gmx_pme_send_resetcounters(cr, step);
+            }
+            /* Correct max_hours for the elapsed time */
+            max_hours                -= elapsed_time/(60.0*60.0);
+            bResetCountersHalfMaxH    = FALSE;
+            gs.set[eglsRESETCOUNTERS] = 0;
+        }
+
+        /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
+        IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
+
+    }
+    /* End of main MD loop */
+    debug_gmx();
+
+    /* Closing TNG files can include compressing data. Therefore it is good to do that
+     * before stopping the time measurements. */
+    mdoutf_tng_close(outf);
+
+    /* Stop measuring walltime */
+    walltime_accounting_end(walltime_accounting);
+
+    if (bRerunMD && MASTER(cr))
+    {
+        close_trj(status);
+    }
+
+    if (!(cr->duty & DUTY_PME))
+    {
+        /* Tell the PME only node to finish */
+        gmx_pme_send_finish(cr);
+    }
+
+    if (MASTER(cr))
+    {
+        if (ir->nstcalcenergy > 0 && !bRerunMD)
+        {
+            print_ebin(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
+                       eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
+        }
+    }
+
+    done_mdoutf(outf);
+    debug_gmx();
+
+    if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
+    {
+        fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
+        fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
+    }
+
+    if (pme_loadbal != NULL)
+    {
+        pme_loadbal_done(pme_loadbal, cr, fplog,
+                         fr->nbv != NULL && fr->nbv->bUseGPU);
+    }
+
+    if (shellfc && fplog)
+    {
+        fprintf(fplog, "Fraction of iterations that converged:           %.2f %%\n",
+                (nconverged*100.0)/step_rel);
+        fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+                tcount/step_rel);
+    }
+
+    if (repl_ex_nst > 0 && MASTER(cr))
+    {
+        print_replica_exchange_statistics(fplog, repl_ex);
+    }
+
+    /* IMD cleanup, if bIMD is TRUE. */
+    IMD_finalize(ir->bIMD, ir->imd);
+
+    walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
+
+    return 0;
+}
diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 6bac3f0..e9fbf48 100644
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -55,6 +55,12 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain; 
+extern void(*plumedcmd)(plumed,const char*,const void*);
+/* END PLUMED */
 
 int gmx_mdrun(int argc, char *argv[])
 {
@@ -428,6 +434,7 @@ int gmx_mdrun(int argc, char *argv[])
         { efMTX, "-mtx",    "nm",       ffOPTWR },
         { efNDX, "-dn",     "dipole",   ffOPTWR },
         { efRND, "-multidir", NULL,      ffOPTRDMULT},
+        { efDAT, "-plumed", "plumed",   ffOPTRD },   /* PLUMED */
         { efDAT, "-membed", "membed",   ffOPTRD },
         { efTOP, "-mp",     "membed",   ffOPTRD },
         { efNDX, "-mn",     "membed",   ffOPTRD },
@@ -780,6 +787,32 @@ int gmx_mdrun(int argc, char *argv[])
     ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
     ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
 
+    /* PLUMED */
+    plumedswitch=0;
+    if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
+    if(plumedswitch){
+      plumedcmd=plumed_cmd;
+      int plumed_is_there=0;
+      int real_precision=sizeof(real);
+      real energyUnits=1.0;
+      real lengthUnits=1.0;
+      real timeUnits=1.0;
+  
+      if(!plumed_installed()){
+        gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
+      }
+      plumedmain=plumed_create();
+      plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
+      // this is not necessary for gromacs units:
+      plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
+      plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
+      plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
+      //
+      plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
+      plumedswitch=1;
+    }
+    /* END PLUMED */
+
     rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
                   nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
                   dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
@@ -788,6 +821,12 @@ int gmx_mdrun(int argc, char *argv[])
                   nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
                   pforce, cpt_period, max_hours, deviceOptions, imdport, Flags);
 
+    /* PLUMED */
+    if(plumedswitch){
+      plumed_finalize(plumedmain);
+    }
+    /* END PLUMED */
+
     /* Log file has to be closed in mdrunner if we are appending to it
        (fplog not set here) */
     if (MASTER(cr) && !bAppendFiles)
diff --git a/src/programs/mdrun/mdrun.cpp.preplumed b/src/programs/mdrun/mdrun.cpp.preplumed
new file mode 100644
index 0000000..6bac3f0
--- /dev/null
+++ b/src/programs/mdrun/mdrun.cpp.preplumed
@@ -0,0 +1,799 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "mdrun_main.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
+
+int gmx_mdrun(int argc, char *argv[])
+{
+    const char   *desc[] = {
+        "[THISMODULE] is the main computational chemistry engine",
+        "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
+        "but it can also perform Stochastic Dynamics, Energy Minimization,",
+        "test particle insertion or (re)calculation of energies.",
+        "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
+        "builds a Hessian matrix from single conformation.",
+        "For usual Normal Modes-like calculations, make sure that",
+        "the structure provided is properly energy-minimized.",
+        "The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
+        "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
+        "and distributes the topology over ranks if needed.",
+        "[TT]mdrun[tt] produces at least four output files.",
+        "A single log file ([TT]-g[tt]) is written, unless the option",
+        "[TT]-seppot[tt] is used, in which case each rank writes a log file.",
+        "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
+        "optionally forces.",
+        "The structure file ([TT]-c[tt]) contains the coordinates and",
+        "velocities of the last step.",
+        "The energy file ([TT]-e[tt]) contains energies, the temperature,",
+        "pressure, etc, a lot of these things are also printed in the log file.",
+        "Optionally coordinates can be written to a compressed trajectory file",
+        "([TT]-x[tt]).[PAR]",
+        "The option [TT]-dhdl[tt] is only used when free energy calculation is",
+        "turned on.[PAR]",
+        "A simulation can be run in parallel using two different parallelization",
+        "schemes: MPI parallelization and/or OpenMP thread parallelization.",
+        "The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
+        "compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
+        "compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
+        "are supported when [TT]mdrun[tt] is compiled with OpenMP. Full OpenMP support",
+        "is only available with the Verlet cut-off scheme, with the (older)",
+        "group scheme only PME-only ranks can use OpenMP parallelization.",
+        "In all cases [TT]mdrun[tt] will by default try to use all the available",
+        "hardware resources. With a normal MPI library only the options",
+        "[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
+        "for PME-only ranks, can be used to control the number of threads.",
+        "With thread-MPI there are additional options [TT]-nt[tt], which sets",
+        "the total number of threads, and [TT]-ntmpi[tt], which sets the number",
+        "of thread-MPI threads.",
+        "The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
+        "the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
+        "The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
+        "the number of threads used by the PME-only ranks.[PAR]",
+        "Note that combined MPI+OpenMP parallelization is in many cases",
+        "slower than either on its own. However, at high parallelization, using the",
+        "combination is often beneficial as it reduces the number of domains and/or",
+        "the number of MPI ranks. (Less and larger domains can improve scaling,",
+        "with separate PME ranks, using fewer MPI ranks reduces communication costs.)",
+        "OpenMP-only parallelization is typically faster than MPI-only parallelization",
+        "on a single CPU(-die). Since we currently don't have proper hardware",
+        "topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
+        "automatically use OpenMP-only parallelization when you use up to 4",
+        "threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
+        "threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
+        "parallelization is used (except with GPUs, see below).",
+        "[PAR]",
+        "To quickly test the performance of the new Verlet cut-off scheme",
+        "with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
+        "the [TT]-testverlet[tt] option. This should not be used for production,",
+        "since it can slightly modify potentials and it will remove charge groups",
+        "making analysis difficult, as the [TT].tpr[tt] file will still contain",
+        "charge groups. For production simulations it is highly recommended",
+        "to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
+        "[PAR]",
+        "With GPUs (only supported with the Verlet cut-off scheme), the number",
+        "of GPUs should match the number of particle-particle ranks, i.e.",
+        "excluding PME-only ranks. With thread-MPI, unless set on the command line, the number",
+        "of MPI threads will automatically be set to the number of GPUs detected.",
+        "To use a subset of the available GPUs, or to manually provide a mapping of",
+        "GPUs to PP ranks, you can use the [TT]-gpu_id[tt] option. The argument of [TT]-gpu_id[tt] is",
+        "a string of digits (without delimiter) representing device id-s of the GPUs to be used.",
+        "For example, \"[TT]02[tt]\" specifies using GPUs 0 and 2 in the first and second PP ranks per compute node",
+        "respectively. To select different sets of GPU-s",
+        "on different nodes of a compute cluster, use the [TT]GMX_GPU_ID[tt] environment",
+        "variable instead. The format for [TT]GMX_GPU_ID[tt] is identical to ",
+        "[TT]-gpu_id[tt], with the difference that an environment variable can have",
+        "different values on different compute nodes. Multiple MPI ranks on each node",
+        "can share GPUs. This is accomplished by specifying the id(s) of the GPU(s)",
+        "multiple times, e.g. \"[TT]0011[tt]\" for four ranks sharing two GPUs in this node.",
+        "This works within a single simulation, or a multi-simulation, with any form of MPI.",
+        "[PAR]",
+        "With the Verlet cut-off scheme and verlet-buffer-tolerance set,",
+        "the pair-list update interval nstlist can be chosen freely with",
+        "the option [TT]-nstlist[tt]. [TT]mdrun[tt] will then adjust",
+        "the pair-list cut-off to maintain accuracy, and not adjust nstlist.",
+        "Otherwise, by default, [TT]mdrun[tt] will try to increase the",
+        "value of nstlist set in the [TT].mdp[tt] file to improve the",
+        "performance. For CPU-only runs, nstlist might increase to 20, for",
+        "GPU runs up to 40. For medium to high parallelization or with",
+        "fast GPUs, a (user-supplied) larger nstlist value can give much",
+        "better performance.",
+        "[PAR]",
+        "When using PME with separate PME ranks or with a GPU, the two major",
+        "compute tasks, the non-bonded force calculation and the PME calculation",
+        "run on different compute resources. If this load is not balanced,",
+        "some of the resources will be idle part of time. With the Verlet",
+        "cut-off scheme this load is automatically balanced when the PME load",
+        "is too high (but not when it is too low). This is done by scaling",
+        "the Coulomb cut-off and PME grid spacing by the same amount. In the first",
+        "few hundred steps different settings are tried and the fastest is chosen",
+        "for the rest of the simulation. This does not affect the accuracy of",
+        "the results, but it does affect the decomposition of the Coulomb energy",
+        "into particle and mesh contributions. The auto-tuning can be turned off",
+        "with the option [TT]-notunepme[tt].",
+        "[PAR]",
+        "[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
+        "when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
+        "even when no multi-threading is used,",
+        "as this usually results in significantly better performance.",
+        "If the queuing systems or the OpenMP library pinned threads, we honor",
+        "this and don't pin again, even though the layout may be sub-optimal.",
+        "If you want to have [TT]mdrun[tt] override an already set thread affinity",
+        "or pin threads when using less cores, use [TT]-pin on[tt].",
+        "With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
+        "there are multiple logical cores per physical core.",
+        "The option [TT]-pinstride[tt] sets the stride in logical cores for",
+        "pinning consecutive threads. Without SMT, 1 is usually the best choice.",
+        "With Intel Hyper-Threading 2 is best when using half or less of the",
+        "logical cores, 1 otherwise. The default value of 0 do exactly that:",
+        "it minimizes the threads per logical core, to optimize performance.",
+        "If you want to run multiple [TT]mdrun[tt] jobs on the same physical node,"
+        "you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
+        "When running multiple [TT]mdrun[tt] (or other) simulations on the same physical",
+        "node, some simulations need to start pinning from a non-zero core",
+        "to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
+        "the offset in logical cores for pinning.",
+        "[PAR]",
+        "When [TT]mdrun[tt] is started with more than 1 rank,",
+        "parallelization with domain decomposition is used.",
+        "[PAR]",
+        "With domain decomposition, the spatial decomposition can be set",
+        "with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
+        "The user only needs to change this when the system is very inhomogeneous.",
+        "Dynamic load balancing is set with the option [TT]-dlb[tt],",
+        "which can give a significant performance improvement,",
+        "especially for inhomogeneous systems. The only disadvantage of",
+        "dynamic load balancing is that runs are no longer binary reproducible,",
+        "but in most cases this is not important.",
+        "By default the dynamic load balancing is automatically turned on",
+        "when the measured performance loss due to load imbalance is 5% or more.",
+        "At low parallelization these are the only important options",
+        "for domain decomposition.",
+        "At high parallelization the options in the next two sections",
+        "could be important for increasing the performace.",
+        "[PAR]",
+        "When PME is used with domain decomposition, separate ranks can",
+        "be assigned to do only the PME mesh calculation;",
+        "this is computationally more efficient starting at about 12 ranks,",
+        "or even fewer when OpenMP parallelization is used.",
+        "The number of PME ranks is set with option [TT]-npme[tt],",
+        "but this cannot be more than half of the ranks.",
+        "By default [TT]mdrun[tt] makes a guess for the number of PME",
+        "ranks when the number of ranks is larger than 16. With GPUs,",
+        "using separate PME ranks is not selected automatically,",
+        "since the optimal setup depends very much on the details",
+        "of the hardware. In all cases, you might gain performance",
+        "by optimizing [TT]-npme[tt]. Performance statistics on this issue",
+        "are written at the end of the log file.",
+        "For good load balancing at high parallelization, the PME grid x and y",
+        "dimensions should be divisible by the number of PME ranks",
+        "(the simulation will run correctly also when this is not the case).",
+        "[PAR]",
+        "This section lists all options that affect the domain decomposition.",
+        "[PAR]",
+        "Option [TT]-rdd[tt] can be used to set the required maximum distance",
+        "for inter charge-group bonded interactions.",
+        "Communication for two-body bonded interactions below the non-bonded",
+        "cut-off distance always comes for free with the non-bonded communication.",
+        "Atoms beyond the non-bonded cut-off are only communicated when they have",
+        "missing bonded interactions; this means that the extra cost is minor",
+        "and nearly indepedent of the value of [TT]-rdd[tt].",
+        "With dynamic load balancing option [TT]-rdd[tt] also sets",
+        "the lower limit for the domain decomposition cell sizes.",
+        "By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
+        "the initial coordinates. The chosen value will be a balance",
+        "between interaction range and communication cost.",
+        "[PAR]",
+        "When inter charge-group bonded interactions are beyond",
+        "the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
+        "For pair interactions and tabulated bonds",
+        "that do not generate exclusions, this check can be turned off",
+        "with the option [TT]-noddcheck[tt].",
+        "[PAR]",
+        "When constraints are present, option [TT]-rcon[tt] influences",
+        "the cell size limit as well.",
+        "Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
+        "should not be beyond the smallest cell size. A error message is",
+        "generated when this happens and the user should change the decomposition",
+        "or decrease the LINCS order and increase the number of LINCS iterations.",
+        "By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
+        "in a conservative fashion. For high parallelization it can be useful",
+        "to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
+        "[PAR]",
+        "The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
+        "of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
+        "the cells can scale down by at least this factor. This option is used",
+        "for the automated spatial decomposition (when not using [TT]-dd[tt])",
+        "as well as for determining the number of grid pulses, which in turn",
+        "sets the minimum allowed cell size. Under certain circumstances",
+        "the value of [TT]-dds[tt] might need to be adjusted to account for",
+        "high or low spatial inhomogeneity of the system.",
+        "[PAR]",
+        "The option [TT]-gcom[tt] can be used to only do global communication",
+        "every n steps.",
+        "This can improve performance for highly parallel simulations",
+        "where this global communication step becomes the bottleneck.",
+        "For a global thermostat and/or barostat the temperature",
+        "and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
+        "By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
+        "With [TT]-rerun[tt] an input trajectory can be given for which ",
+        "forces and energies will be (re)calculated. Neighbor searching will be",
+        "performed for every frame, unless [TT]nstlist[tt] is zero",
+        "(see the [TT].mdp[tt] file).[PAR]",
+        "ED (essential dynamics) sampling and/or additional flooding potentials",
+        "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
+        "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+        "or by using options in the essdyn menu of the WHAT IF program.",
+        "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+        "contains projections of positions, velocities and forces onto selected",
+        "eigenvectors.[PAR]",
+        "When user-defined potential functions have been selected in the",
+        "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+        "a formatted table with potential functions. The file is read from",
+        "either the current directory or from the [TT]GMXLIB[tt] directory.",
+        "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
+        "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
+        "normal Coulomb.",
+        "When pair interactions are present, a separate table for pair interaction",
+        "functions is read using the [TT]-tablep[tt] option.[PAR]",
+        "When tabulated bonded functions are present in the topology,",
+        "interaction functions are read using the [TT]-tableb[tt] option.",
+        "For each different tabulated interaction type the table file name is",
+        "modified in a different way: before the file extension an underscore is",
+        "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
+        "and finally the table number of the interaction type.[PAR]",
+        "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
+        "coordinates and forces when pulling is selected",
+        "in the [TT].mdp[tt] file.[PAR]",
+        "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
+        "simulated in parallel.",
+        "As many input files/directories are required as the number of systems. ",
+        "The [TT]-multidir[tt] option takes a list of directories (one for each ",
+        "system) and runs in each of them, using the input/output file names, ",
+        "such as specified by e.g. the [TT]-s[tt] option, relative to these ",
+        "directories.",
+        "With [TT]-multi[tt], the system number is appended to the run input ",
+        "and each output filename, for instance [TT]topol.tpr[tt] becomes",
+        "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
+        "The number of ranks per system is the total number of ranks",
+        "divided by the number of systems.",
+        "One use of this option is for NMR refinement: when distance",
+        "or orientation restraints are present these can be ensemble averaged",
+        "over all the systems.[PAR]",
+        "With [TT]-replex[tt] replica exchange is attempted every given number",
+        "of steps. The number of replicas is set with the [TT]-multi[tt] or ",
+        "[TT]-multidir[tt] option, described above.",
+        "All run input files should use a different coupling temperature,",
+        "the order of the files is not important. The random seed is set with",
+        "[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
+        "is performed after every exchange.[PAR]",
+        "Finally some experimental algorithms can be tested when the",
+        "appropriate options have been given. Currently under",
+        "investigation are: polarizability.",
+        "[PAR]",
+        "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
+        "a protein into a membrane. The data file should contain the options",
+        "that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
+        "both apply to this as well.",
+        "[PAR]",
+        "The option [TT]-pforce[tt] is useful when you suspect a simulation",
+        "crashes due to too large forces. With this option coordinates and",
+        "forces of atoms with a force larger than a certain value will",
+        "be printed to stderr.",
+        "[PAR]",
+        "Checkpoints containing the complete state of the system are written",
+        "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
+        "unless option [TT]-cpt[tt] is set to -1.",
+        "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
+        "make sure that a recent state of the system is always available,",
+        "even when the simulation is terminated while writing a checkpoint.",
+        "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
+        "with the step number.",
+        "A simulation can be continued by reading the full state from file",
+        "with option [TT]-cpi[tt]. This option is intelligent in the way that",
+        "if no checkpoint file is found, Gromacs just assumes a normal run and",
+        "starts from the first step of the [TT].tpr[tt] file. By default the output",
+        "will be appending to the existing output files. The checkpoint file",
+        "contains checksums of all output files, such that you will never",
+        "loose data when some output files are modified, corrupt or removed.",
+        "There are three scenarios with [TT]-cpi[tt]:[PAR]",
+        "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
+        "[TT]*[tt] all files are present with names and checksums matching those stored",
+        "in the checkpoint file: files are appended[PAR]",
+        "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
+        "With [TT]-noappend[tt] new output files are opened and the simulation",
+        "part number is added to all output file names.",
+        "Note that in all cases the checkpoint file itself is not renamed",
+        "and will be overwritten, unless its name does not match",
+        "the [TT]-cpo[tt] option.",
+        "[PAR]",
+        "With checkpointing the output is appended to previously written",
+        "output files, unless [TT]-noappend[tt] is used or none of the previous",
+        "output files are present (except for the checkpoint file).",
+        "The integrity of the files to be appended is verified using checksums",
+        "which are stored in the checkpoint file. This ensures that output can",
+        "not be mixed up or corrupted due to file appending. When only some",
+        "of the previous output files are present, a fatal error is generated",
+        "and no old output files are modified and no new output files are opened.",
+        "The result with appending will be the same as from a single run.",
+        "The contents will be binary identical, unless you use a different number",
+        "of ranks or dynamic load balancing or the FFT library uses optimizations",
+        "through timing.",
+        "[PAR]",
+        "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
+        "file is written at the first neighbor search step where the run time",
+        "exceeds [TT]-maxh[tt]*0.99 hours.",
+        "[PAR]",
+        "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
+        "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
+        "pressed), it will stop after the next neighbor search step ",
+        "(with nstlist=0 at the next step).",
+        "In both cases all the usual output will be written to file.",
+        "When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
+        "is sufficient, this signal should not be sent to mpirun or",
+        "the [TT]mdrun[tt] process that is the parent of the others.",
+        "[PAR]",
+        "Interactive molecular dynamics (IMD) can be activated by using at least one",
+        "of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate the",
+        "simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
+        "[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
+        "IMD remote can be turned on by [TT]-imdpull[tt].",
+        "The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
+        "file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
+        "pulling is used."
+        "[PAR]",
+        "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
+    };
+    t_commrec    *cr;
+    t_filenm      fnm[] = {
+        { efTPX, NULL,      NULL,       ffREAD },
+        { efTRN, "-o",      NULL,       ffWRITE },
+        { efCOMPRESSED, "-x", NULL,     ffOPTWR },
+        { efCPT, "-cpi",    NULL,       ffOPTRD },
+        { efCPT, "-cpo",    NULL,       ffOPTWR },
+        { efSTO, "-c",      "confout",  ffWRITE },
+        { efEDR, "-e",      "ener",     ffWRITE },
+        { efLOG, "-g",      "md",       ffWRITE },
+        { efXVG, "-dhdl",   "dhdl",     ffOPTWR },
+        { efXVG, "-field",  "field",    ffOPTWR },
+        { efXVG, "-table",  "table",    ffOPTRD },
+        { efXVG, "-tabletf", "tabletf",    ffOPTRD },
+        { efXVG, "-tablep", "tablep",   ffOPTRD },
+        { efXVG, "-tableb", "table",    ffOPTRD },
+        { efTRX, "-rerun",  "rerun",    ffOPTRD },
+        { efXVG, "-tpi",    "tpi",      ffOPTWR },
+        { efXVG, "-tpid",   "tpidist",  ffOPTWR },
+        { efEDI, "-ei",     "sam",      ffOPTRD },
+        { efXVG, "-eo",     "edsam",    ffOPTWR },
+        { efXVG, "-devout", "deviatie", ffOPTWR },
+        { efXVG, "-runav",  "runaver",  ffOPTWR },
+        { efXVG, "-px",     "pullx",    ffOPTWR },
+        { efXVG, "-pf",     "pullf",    ffOPTWR },
+        { efXVG, "-ro",     "rotation", ffOPTWR },
+        { efLOG, "-ra",     "rotangles", ffOPTWR },
+        { efLOG, "-rs",     "rotslabs", ffOPTWR },
+        { efLOG, "-rt",     "rottorque", ffOPTWR },
+        { efMTX, "-mtx",    "nm",       ffOPTWR },
+        { efNDX, "-dn",     "dipole",   ffOPTWR },
+        { efRND, "-multidir", NULL,      ffOPTRDMULT},
+        { efDAT, "-membed", "membed",   ffOPTRD },
+        { efTOP, "-mp",     "membed",   ffOPTRD },
+        { efNDX, "-mn",     "membed",   ffOPTRD },
+        { efXVG, "-if",     "imdforces", ffOPTWR },
+        { efXVG, "-swap",   "swapions", ffOPTWR }
+    };
+#define NFILE asize(fnm)
+
+    /* Command line options ! */
+    gmx_bool        bDDBondCheck  = TRUE;
+    gmx_bool        bDDBondComm   = TRUE;
+    gmx_bool        bTunePME      = TRUE;
+    gmx_bool        bTestVerlet   = FALSE;
+    gmx_bool        bVerbose      = FALSE;
+    gmx_bool        bCompact      = TRUE;
+    gmx_bool        bSepPot       = FALSE;
+    gmx_bool        bRerunVSite   = FALSE;
+    gmx_bool        bConfout      = TRUE;
+    gmx_bool        bReproducible = FALSE;
+    gmx_bool        bIMDwait      = FALSE;
+    gmx_bool        bIMDterm      = FALSE;
+    gmx_bool        bIMDpull      = FALSE;
+
+    int             npme          = -1;
+    int             nstlist       = 0;
+    int             nmultisim     = 0;
+    int             nstglobalcomm = -1;
+    int             repl_ex_nst   = 0;
+    int             repl_ex_seed  = -1;
+    int             repl_ex_nex   = 0;
+    int             nstepout      = 100;
+    int             resetstep     = -1;
+    gmx_int64_t     nsteps        = -2;   /* the value -2 means that the mdp option will be used */
+    int             imdport       = 8888; /* can be almost anything, 8888 is easy to remember */
+
+    rvec            realddxyz          = {0, 0, 0};
+    const char     *ddno_opt[ddnoNR+1] =
+    { NULL, "interleave", "pp_pme", "cartesian", NULL };
+    const char     *dddlb_opt[] =
+    { NULL, "auto", "no", "yes", NULL };
+    const char     *thread_aff_opt[threadaffNR+1] =
+    { NULL, "auto", "on", "off", NULL };
+    const char     *nbpu_opt[] =
+    { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
+    real            rdd                   = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
+    char           *ddcsx                 = NULL, *ddcsy = NULL, *ddcsz = NULL;
+    real            cpt_period            = 15.0, max_hours = -1;
+    gmx_bool        bAppendFiles          = TRUE;
+    gmx_bool        bKeepAndNumCPT        = FALSE;
+    gmx_bool        bResetCountersHalfWay = FALSE;
+    output_env_t    oenv                  = NULL;
+    const char     *deviceOptions         = "";
+
+    /* Non transparent initialization of a complex gmx_hw_opt_t struct.
+     * But unfortunately we are not allowed to call a function here,
+     * since declarations follow below.
+     */
+    gmx_hw_opt_t    hw_opt = {
+        0, 0, 0, 0, threadaffSEL, 0, 0,
+        { NULL, FALSE, 0, NULL }
+    };
+
+    t_pargs         pa[] = {
+
+        { "-dd",      FALSE, etRVEC, {&realddxyz},
+          "Domain decomposition grid, 0 is optimize" },
+        { "-ddorder", FALSE, etENUM, {ddno_opt},
+          "DD rank order" },
+        { "-npme",    FALSE, etINT, {&npme},
+          "Number of separate ranks to be used for PME, -1 is guess" },
+        { "-nt",      FALSE, etINT, {&hw_opt.nthreads_tot},
+          "Total number of threads to start (0 is guess)" },
+        { "-ntmpi",   FALSE, etINT, {&hw_opt.nthreads_tmpi},
+          "Number of thread-MPI threads to start (0 is guess)" },
+        { "-ntomp",   FALSE, etINT, {&hw_opt.nthreads_omp},
+          "Number of OpenMP threads per MPI rank to start (0 is guess)" },
+        { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
+          "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
+        { "-pin",     FALSE, etENUM, {thread_aff_opt},
+          "Set thread affinities" },
+        { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
+          "The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
+        { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
+          "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
+        { "-gpu_id",  FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
+          "List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
+        { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+          "Check for all bonded interactions with DD" },
+        { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
+          "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+        { "-rdd",     FALSE, etREAL, {&rdd},
+          "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+        { "-rcon",    FALSE, etREAL, {&rconstr},
+          "Maximum distance for P-LINCS (nm), 0 is estimate" },
+        { "-dlb",     FALSE, etENUM, {dddlb_opt},
+          "Dynamic load balancing (with DD)" },
+        { "-dds",     FALSE, etREAL, {&dlb_scale},
+          "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
+          "provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
+        { "-ddcsx",   FALSE, etSTR, {&ddcsx},
+          "HIDDENA string containing a vector of the relative sizes in the x "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-ddcsy",   FALSE, etSTR, {&ddcsy},
+          "HIDDENA string containing a vector of the relative sizes in the y "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-ddcsz",   FALSE, etSTR, {&ddcsz},
+          "HIDDENA string containing a vector of the relative sizes in the z "
+          "direction of the corresponding DD cells. Only effective with static "
+          "load balancing." },
+        { "-gcom",    FALSE, etINT, {&nstglobalcomm},
+          "Global communication frequency" },
+        { "-nb",      FALSE, etENUM, {&nbpu_opt},
+          "Calculate non-bonded interactions on" },
+        { "-nstlist", FALSE, etINT, {&nstlist},
+          "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
+        { "-tunepme", FALSE, etBOOL, {&bTunePME},
+          "Optimize PME load between PP/PME ranks or GPU/CPU" },
+        { "-testverlet", FALSE, etBOOL, {&bTestVerlet},
+          "Test the Verlet non-bonded scheme" },
+        { "-v",       FALSE, etBOOL, {&bVerbose},
+          "Be loud and noisy" },
+        { "-compact", FALSE, etBOOL, {&bCompact},
+          "Write a compact log file" },
+        { "-seppot",  FALSE, etBOOL, {&bSepPot},
+          "Write separate V and dVdl terms for each interaction type and rank to the log file(s)" },
+        { "-pforce",  FALSE, etREAL, {&pforce},
+          "Print all forces larger than this (kJ/mol nm)" },
+        { "-reprod",  FALSE, etBOOL, {&bReproducible},
+          "Try to avoid optimizations that affect binary reproducibility" },
+        { "-cpt",     FALSE, etREAL, {&cpt_period},
+          "Checkpoint interval (minutes)" },
+        { "-cpnum",   FALSE, etBOOL, {&bKeepAndNumCPT},
+          "Keep and number checkpoint files" },
+        { "-append",  FALSE, etBOOL, {&bAppendFiles},
+          "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
+        { "-nsteps",  FALSE, etINT64, {&nsteps},
+          "Run this number of steps, overrides .mdp file option" },
+        { "-maxh",   FALSE, etREAL, {&max_hours},
+          "Terminate after 0.99 times this time (hours)" },
+        { "-multi",   FALSE, etINT, {&nmultisim},
+          "Do multiple simulations in parallel" },
+        { "-replex",  FALSE, etINT, {&repl_ex_nst},
+          "Attempt replica exchange periodically with this period (steps)" },
+        { "-nex",  FALSE, etINT, {&repl_ex_nex},
+          "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion).  -nex zero or not specified gives neighbor replica exchange." },
+        { "-reseed",  FALSE, etINT, {&repl_ex_seed},
+          "Seed for replica exchange, -1 is generate a seed" },
+        { "-imdport",    FALSE, etINT, {&imdport},
+          "HIDDENIMD listening port" },
+        { "-imdwait",  FALSE, etBOOL, {&bIMDwait},
+          "HIDDENPause the simulation while no IMD client is connected" },
+        { "-imdterm",  FALSE, etBOOL, {&bIMDterm},
+          "HIDDENAllow termination of the simulation from IMD client" },
+        { "-imdpull",  FALSE, etBOOL, {&bIMDpull},
+          "HIDDENAllow pulling in the simulation from IMD client" },
+        { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
+          "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+        { "-confout", FALSE, etBOOL, {&bConfout},
+          "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+        { "-stepout", FALSE, etINT, {&nstepout},
+          "HIDDENFrequency of writing the remaining wall clock time for the run" },
+        { "-resetstep", FALSE, etINT, {&resetstep},
+          "HIDDENReset cycle counters after these many time steps" },
+        { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
+          "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+    };
+    unsigned long   Flags, PCA_Flags;
+    ivec            ddxyz;
+    int             dd_node_order;
+    gmx_bool        bAddPart;
+    FILE           *fplog, *fpmulti;
+    int             sim_part, sim_part_fn;
+    const char     *part_suffix = ".part";
+    char            suffix[STRLEN];
+    int             rc;
+    char          **multidir = NULL;
+
+
+    cr = init_commrec();
+
+    PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
+
+    /* Comment this in to do fexist calls only on master
+     * works not with rerun or tables at the moment
+     * also comment out the version of init_forcerec in md.c
+     * with NULL instead of opt2fn
+     */
+    /*
+       if (!MASTER(cr))
+       {
+       PCA_Flags |= PCA_NOT_READ_NODE;
+       }
+     */
+
+    if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
+                           asize(desc), desc, 0, NULL, &oenv))
+    {
+        return 0;
+    }
+
+
+    /* we set these early because they might be used in init_multisystem()
+       Note that there is the potential for npme>nnodes until the number of
+       threads is set later on, if there's thread parallelization. That shouldn't
+       lead to problems. */
+    dd_node_order = nenum(ddno_opt);
+    cr->npmenodes = npme;
+
+    hw_opt.thread_affinity = nenum(thread_aff_opt);
+
+    /* now check the -multi and -multidir option */
+    if (opt2bSet("-multidir", NFILE, fnm))
+    {
+        if (nmultisim > 0)
+        {
+            gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
+        }
+        nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
+    }
+
+
+    if (repl_ex_nst != 0 && nmultisim < 2)
+    {
+        gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
+    }
+
+    if (repl_ex_nex < 0)
+    {
+        gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+    }
+
+    if (nmultisim > 1)
+    {
+#ifndef GMX_THREAD_MPI
+        gmx_bool bParFn = (multidir == NULL);
+        init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
+#else
+        gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library. "
+                  "Please compile GROMACS with MPI support");
+#endif
+    }
+
+    bAddPart = !bAppendFiles;
+
+    /* Check if there is ANY checkpoint file available */
+    sim_part    = 1;
+    sim_part_fn = sim_part;
+    if (opt2bSet("-cpi", NFILE, fnm))
+    {
+        if (bSepPot && bAppendFiles)
+        {
+            gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
+        }
+
+        bAppendFiles =
+            read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
+                                                          fnm, cr),
+                                            &sim_part_fn, NULL, cr,
+                                            bAppendFiles, NFILE, fnm,
+                                            part_suffix, &bAddPart);
+        if (sim_part_fn == 0 && MULTIMASTER(cr))
+        {
+            fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
+        }
+        else
+        {
+            sim_part = sim_part_fn + 1;
+        }
+
+        if (MULTISIM(cr) && MASTER(cr))
+        {
+            if (MULTIMASTER(cr))
+            {
+                /* Log file is not yet available, so if there's a
+                 * problem we can only write to stderr. */
+                fpmulti = stderr;
+            }
+            else
+            {
+                fpmulti = NULL;
+            }
+            check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
+        }
+    }
+    else
+    {
+        bAppendFiles = FALSE;
+    }
+
+    if (!bAppendFiles)
+    {
+        sim_part_fn = sim_part;
+    }
+
+    if (bAddPart)
+    {
+        /* Rename all output files (except checkpoint files) */
+        /* create new part name first (zero-filled) */
+        sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
+
+        add_suffix_to_output_names(fnm, NFILE, suffix);
+        if (MULTIMASTER(cr))
+        {
+            fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
+        }
+    }
+
+    Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
+    Flags = Flags | (bSepPot       ? MD_SEPPOT       : 0);
+    Flags = Flags | (bDDBondCheck  ? MD_DDBONDCHECK  : 0);
+    Flags = Flags | (bDDBondComm   ? MD_DDBONDCOMM   : 0);
+    Flags = Flags | (bTunePME      ? MD_TUNEPME      : 0);
+    Flags = Flags | (bTestVerlet   ? MD_TESTVERLET   : 0);
+    Flags = Flags | (bConfout      ? MD_CONFOUT      : 0);
+    Flags = Flags | (bRerunVSite   ? MD_RERUN_VSITE  : 0);
+    Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
+    Flags = Flags | (bAppendFiles  ? MD_APPENDFILES  : 0);
+    Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
+    Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
+    Flags = Flags | (sim_part > 1    ? MD_STARTFROMCPT : 0);
+    Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
+    Flags = Flags | (bIMDwait      ? MD_IMDWAIT      : 0);
+    Flags = Flags | (bIMDterm      ? MD_IMDTERM      : 0);
+    Flags = Flags | (bIMDpull      ? MD_IMDPULL      : 0);
+
+    /* We postpone opening the log file if we are appending, so we can
+       first truncate the old log file and append to the correct position
+       there instead.  */
+    if ((MASTER(cr) || bSepPot) && !bAppendFiles)
+    {
+        gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
+                     !bSepPot, Flags & MD_APPENDFILES, &fplog);
+        please_cite(fplog, "Hess2008b");
+        please_cite(fplog, "Spoel2005a");
+        please_cite(fplog, "Lindahl2001a");
+        please_cite(fplog, "Berendsen95a");
+    }
+    else if (!MASTER(cr) && bSepPot)
+    {
+        gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
+    }
+    else
+    {
+        fplog = NULL;
+    }
+
+    ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+    ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+    ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+
+    rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
+                  nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
+                  dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
+                  nbpu_opt[0], nstlist,
+                  nsteps, nstepout, resetstep,
+                  nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
+                  pforce, cpt_period, max_hours, deviceOptions, imdport, Flags);
+
+    /* Log file has to be closed in mdrunner if we are appending to it
+       (fplog not set here) */
+    if (MASTER(cr) && !bAppendFiles)
+    {
+        gmx_log_close(fplog);
+    }
+
+    return rc;
+}
diff --git a/src/programs/mdrun/repl_ex.c b/src/programs/mdrun/repl_ex.c
index 46a9bc0..cfb0b7f 100644
--- a/src/programs/mdrun/repl_ex.c
+++ b/src/programs/mdrun/repl_ex.c
@@ -51,6 +51,12 @@
 #include "domdec.h"
 #include "gromacs/random/random.h"
 
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
 #define PROBABILITYCUTOFF 100
 /* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
 
@@ -112,14 +118,16 @@ static gmx_bool repl_quantity(const gmx_multisim_t *ms,
     qall[re->repl] = q;
     gmx_sum_sim(ms->nsim, qall, ms);
 
-    bDiff = FALSE;
-    for (s = 1; s < ms->nsim; s++)
-    {
-        if (qall[s] != qall[0])
-        {
+    /* PLUMED */
+    //bDiff = FALSE;
+    //for (s = 1; s < ms->nsim; s++)
+    //{
+    //    if (qall[s] != qall[0])
+    //    {
             bDiff = TRUE;
-        }
-    }
+    //    }
+    //}
+    /* END PLUMED */
 
     if (bDiff)
     {
@@ -269,6 +277,10 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
         re->ind[i] = i;
     }
 
+    /* PLUMED */
+    // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
+    // in those cases replicas can share the same temperature.
+    /*
     if (re->type < ereENDSINGLE)
     {
 
@@ -277,11 +289,12 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
             for (j = i+1; j < re->nrepl; j++)
             {
                 if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
-                {
+                {*/
                     /* Unordered replicas are supposed to work, but there
                      * is still an issues somewhere.
                      * Note that at this point still re->ind[i]=i.
                      */
+                 /*
                     gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
                               i, j,
                               erename[re->type],
@@ -299,6 +312,8 @@ gmx_repl_ex_t init_replica_exchange(FILE *fplog,
             }
         }
     }
+    */
+    /* END PLUMED */
 
     /* keep track of all the swaps, starting with the initial placement. */
     snew(re->allswaps, re->nrepl);
@@ -982,6 +997,10 @@ test_for_replica_exchange(FILE                 *fplog,
         pind[i] = re->ind[i];
     }
 
+    /* PLUMED */
+    int plumed_test_exchange_pattern=0;
+    /* END PLUMED */
+
     if (bMultiEx)
     {
         /* multiple random switch exchange */
@@ -1057,6 +1076,31 @@ test_for_replica_exchange(FILE                 *fplog,
         /* standard nearest neighbor replica exchange */
 
         m = (step / re->nst) % 2;
+        /* PLUMED */
+        if(plumedswitch){
+          int partner=re->repl;
+          plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
+          if(plumed_test_exchange_pattern>0){
+            int *list;
+            snew(list,re->nrepl);
+            plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
+            plumed_cmd(plumedmain,"getExchangesList",list);
+            for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
+            sfree(list);
+          }
+
+          for(i=1; i<re->nrepl; i++) {
+            if (i % 2 != m) continue;
+            a = re->ind[i-1];
+            b = re->ind[i];
+            if(re->repl==a) partner=b;
+            if(re->repl==b) partner=a;
+          }
+          plumed_cmd(plumedmain,"GREX setPartner",&partner);
+          plumed_cmd(plumedmain,"GREX calculate",NULL);
+          plumed_cmd(plumedmain,"GREX shareAllDeltaBias",NULL);
+        }
+        /* END PLUMED */
         for (i = 1; i < re->nrepl; i++)
         {
             a = re->ind[i-1];
@@ -1066,6 +1110,18 @@ test_for_replica_exchange(FILE                 *fplog,
             if (i % 2 == m)
             {
                 delta = calc_delta(fplog, bPrint, re, a, b, a, b);
+                /* PLUMED */
+                if(plumedswitch){
+                  real adb,bdb,dplumed;
+                  char buf[300];
+                  sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
+                  sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
+                  dplumed=adb*re->beta[a]+bdb*re->beta[b];
+                  delta+=dplumed;
+                  if (bPrint)
+                    fprintf(fplog,"dplumed = %10.3e  dE_Term = %10.3e (kT)\n",dplumed,delta);
+                }
+                /* END PLUMED */
                 if (delta <= 0)
                 {
                     /* accepted */
@@ -1092,11 +1148,22 @@ test_for_replica_exchange(FILE                 *fplog,
 
                 if (bEx[i])
                 {
+                  /* PLUMED */
+                  if(!plumed_test_exchange_pattern) {
+                    /* standard neighbour swapping */
                     /* swap these two */
                     tmp       = pind[i-1];
                     pind[i-1] = pind[i];
                     pind[i]   = tmp;
                     re->nexchange[i]++;  /* statistics for back compatibility */
+                  } else {
+                    /* alternative swapping patterns */
+                    tmp       = pind[a];
+                    pind[a]   = pind[b];
+                    pind[b]   = tmp;
+                    re->nexchange[i]++;  /* statistics for back compatibility */
+                  }
+                  /* END PLUMED */
                 }
             }
             else
@@ -1112,6 +1179,15 @@ test_for_replica_exchange(FILE                 *fplog,
         re->nattempt[m]++;
     }
 
+    /* PLUMED */
+    if(plumed_test_exchange_pattern>0) {
+      for (i = 0; i < re->nrepl; i++)
+      {
+          re->ind[i] = i;
+      }
+    }
+    /* END PLUMED */
+
     /* record which moves were made and accepted */
     for (i = 0; i < re->nrepl; i++)
     {
@@ -1316,6 +1392,10 @@ gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *
     /* The order in which multiple exchanges will occur. */
     gmx_bool bThisReplicaExchanged = FALSE;
 
+    /* PLUMED */
+    if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",NULL);
+    /* END PLUMED */
+
     if (MASTER(cr))
     {
         replica_id  = re->repl;
diff --git a/src/programs/mdrun/repl_ex.c.preplumed b/src/programs/mdrun/repl_ex.c.preplumed
new file mode 100644
index 0000000..46a9bc0
--- /dev/null
+++ b/src/programs/mdrun/repl_ex.c.preplumed
@@ -0,0 +1,1439 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include "repl_ex.h"
+#include "network.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
+#include "physics.h"
+#include "copyrite.h"
+#include "macros.h"
+#include "vec.h"
+#include "names.h"
+#include "domdec.h"
+#include "gromacs/random/random.h"
+
+#define PROBABILITYCUTOFF 100
+/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
+
+enum {
+    ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
+};
+const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
+/* end_single_marker merely notes the end of single variable replica exchange. All types higher than
+   it are multiple replica exchange methods */
+/* Eventually, should add 'pressure', 'temperature and pressure', 'lambda_and_pressure', 'temperature_lambda_pressure'?;
+   Let's wait until we feel better about the pressure control methods giving exact ensembles.  Right now, we assume constant pressure  */
+
+typedef struct gmx_repl_ex
+{
+    int       repl;
+    int       nrepl;
+    real      temp;
+    int       type;
+    real    **q;
+    gmx_bool  bNPT;
+    real     *pres;
+    int      *ind;
+    int      *allswaps;
+    int       nst;
+    int       nex;
+    int       seed;
+    int       nattempt[2];
+    real     *prob_sum;
+    int     **nmoves;
+    int      *nexchange;
+    gmx_rng_t rng;
+
+    /* these are helper arrays for replica exchange; allocated here so they
+       don't have to be allocated each time */
+    int      *destinations;
+    int     **cyclic;
+    int     **order;
+    int      *tmpswap;
+    gmx_bool *incycle;
+    gmx_bool *bEx;
+
+    /* helper arrays to hold the quantities that are exchanged */
+    real  *prob;
+    real  *Epot;
+    real  *beta;
+    real  *Vol;
+    real **de;
+
+} t_gmx_repl_ex;
+
+static gmx_bool repl_quantity(const gmx_multisim_t *ms,
+                              struct gmx_repl_ex *re, int ere, real q)
+{
+    real    *qall;
+    gmx_bool bDiff;
+    int      i, s;
+
+    snew(qall, ms->nsim);
+    qall[re->repl] = q;
+    gmx_sum_sim(ms->nsim, qall, ms);
+
+    bDiff = FALSE;
+    for (s = 1; s < ms->nsim; s++)
+    {
+        if (qall[s] != qall[0])
+        {
+            bDiff = TRUE;
+        }
+    }
+
+    if (bDiff)
+    {
+        /* Set the replica exchange type and quantities */
+        re->type = ere;
+
+        snew(re->q[ere], re->nrepl);
+        for (s = 0; s < ms->nsim; s++)
+        {
+            re->q[ere][s] = qall[s];
+        }
+    }
+    sfree(qall);
+    return bDiff;
+}
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+                                    const gmx_multisim_t *ms,
+                                    const t_state *state,
+                                    const t_inputrec *ir,
+                                    int nst, int nex, int init_seed)
+{
+    real                temp, pres;
+    int                 i, j, k;
+    struct gmx_repl_ex *re;
+    gmx_bool            bTemp;
+    gmx_bool            bLambda = FALSE;
+
+    fprintf(fplog, "\nInitializing Replica Exchange\n");
+
+    if (ms == NULL || ms->nsim == 1)
+    {
+        gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
+    }
+    if (!EI_DYNAMICS(ir->eI))
+    {
+        gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
+        /* Note that PAR(cr) is defined by cr->nnodes > 1, which is
+         * distinct from MULTISIM(cr). A multi-simulation only runs
+         * with real MPI parallelism, but this does not imply PAR(cr)
+         * is true!
+         *
+         * Since we are using a dynamical integrator, the only
+         * decomposition is DD, so PAR(cr) and DOMAINDECOMP(cr) are
+         * synonymous. The only way for cr->nnodes > 1 to be true is
+         * if we are using DD. */
+    }
+
+    snew(re, 1);
+
+    re->repl     = ms->sim;
+    re->nrepl    = ms->nsim;
+    snew(re->q, ereENDSINGLE);
+
+    fprintf(fplog, "Repl  There are %d replicas:\n", re->nrepl);
+
+    check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
+    check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
+    check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
+    check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
+                      "first exchange step: init_step/-replex", FALSE);
+    check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
+    check_multi_int(fplog, ms, ir->opts.ngtc,
+                    "the number of temperature coupling groups", FALSE);
+    check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
+    check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
+    check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
+
+    re->temp = ir->opts.ref_t[0];
+    for (i = 1; (i < ir->opts.ngtc); i++)
+    {
+        if (ir->opts.ref_t[i] != re->temp)
+        {
+            fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+            fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
+        }
+    }
+
+    re->type = -1;
+    bTemp    = repl_quantity(ms, re, ereTEMP, re->temp);
+    if (ir->efep != efepNO)
+    {
+        bLambda = repl_quantity(ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
+    }
+    if (re->type == -1)  /* nothing was assigned */
+    {
+        gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
+    }
+    if (bLambda && bTemp)
+    {
+        re->type = ereTL;
+    }
+
+    if (bTemp)
+    {
+        please_cite(fplog, "Sugita1999a");
+        if (ir->epc != epcNO)
+        {
+            re->bNPT = TRUE;
+            fprintf(fplog, "Repl  Using Constant Pressure REMD.\n");
+            please_cite(fplog, "Okabe2001a");
+        }
+        if (ir->etc == etcBERENDSEN)
+        {
+            gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
+                      ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+        }
+    }
+    if (bLambda)
+    {
+        if (ir->fepvals->delta_lambda != 0)   /* check this? */
+        {
+            gmx_fatal(FARGS, "delta_lambda is not zero");
+        }
+    }
+    if (re->bNPT)
+    {
+        snew(re->pres, re->nrepl);
+        if (ir->epct == epctSURFACETENSION)
+        {
+            pres = ir->ref_p[ZZ][ZZ];
+        }
+        else
+        {
+            pres = 0;
+            j    = 0;
+            for (i = 0; i < DIM; i++)
+            {
+                if (ir->compress[i][i] != 0)
+                {
+                    pres += ir->ref_p[i][i];
+                    j++;
+                }
+            }
+            pres /= j;
+        }
+        re->pres[re->repl] = pres;
+        gmx_sum_sim(re->nrepl, re->pres, ms);
+    }
+
+    /* Make an index for increasing replica order */
+    /* only makes sense if one or the other is varying, not both!
+       if both are varying, we trust the order the person gave. */
+    snew(re->ind, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->ind[i] = i;
+    }
+
+    if (re->type < ereENDSINGLE)
+    {
+
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = i+1; j < re->nrepl; j++)
+            {
+                if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
+                {
+                    /* Unordered replicas are supposed to work, but there
+                     * is still an issues somewhere.
+                     * Note that at this point still re->ind[i]=i.
+                     */
+                    gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
+                              i, j,
+                              erename[re->type],
+                              re->q[re->type][i], re->q[re->type][j],
+                              erename[re->type]);
+
+                    k          = re->ind[i];
+                    re->ind[i] = re->ind[j];
+                    re->ind[j] = k;
+                }
+                else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
+                {
+                    gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
+                }
+            }
+        }
+    }
+
+    /* keep track of all the swaps, starting with the initial placement. */
+    snew(re->allswaps, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->allswaps[i] = re->ind[i];
+    }
+
+    switch (re->type)
+    {
+        case ereTEMP:
+            fprintf(fplog, "\nReplica exchange in temperature\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            break;
+        case ereLAMBDA:
+            fprintf(fplog, "\nReplica exchange in lambda\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            break;
+        case ereTL:
+            fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            break;
+        default:
+            gmx_incons("Unknown replica exchange quantity");
+    }
+    if (re->bNPT)
+    {
+        fprintf(fplog, "\nRepl  p");
+        for (i = 0; i < re->nrepl; i++)
+        {
+            fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
+        }
+
+        for (i = 0; i < re->nrepl; i++)
+        {
+            if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
+            {
+                fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+                fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
+            }
+        }
+    }
+    re->nst = nst;
+    if (init_seed == -1)
+    {
+        if (MASTERSIM(ms))
+        {
+            re->seed = (int)gmx_rng_make_seed();
+        }
+        else
+        {
+            re->seed = 0;
+        }
+        gmx_sumi_sim(1, &(re->seed), ms);
+    }
+    else
+    {
+        re->seed = init_seed;
+    }
+    fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
+    fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
+    re->rng = gmx_rng_init(re->seed);
+
+    re->nattempt[0] = 0;
+    re->nattempt[1] = 0;
+
+    snew(re->prob_sum, re->nrepl);
+    snew(re->nexchange, re->nrepl);
+    snew(re->nmoves, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->nmoves[i], re->nrepl);
+    }
+    fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
+
+    /* generate space for the helper functions so we don't have to snew each time */
+
+    snew(re->destinations, re->nrepl);
+    snew(re->incycle, re->nrepl);
+    snew(re->tmpswap, re->nrepl);
+    snew(re->cyclic, re->nrepl);
+    snew(re->order, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->cyclic[i], re->nrepl);
+        snew(re->order[i], re->nrepl);
+    }
+    /* allocate space for the functions storing the data for the replicas */
+    /* not all of these arrays needed in all cases, but they don't take
+       up much space, since the max size is nrepl**2 */
+    snew(re->prob, re->nrepl);
+    snew(re->bEx, re->nrepl);
+    snew(re->beta, re->nrepl);
+    snew(re->Vol, re->nrepl);
+    snew(re->Epot, re->nrepl);
+    snew(re->de, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->de[i], re->nrepl);
+    }
+    re->nex = nex;
+    return re;
+}
+
+static void exchange_reals(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, real *v, int n)
+{
+    real *buf;
+    int   i;
+
+    if (v)
+    {
+        snew(buf, n);
+#ifdef GMX_MPI
+        /*
+           MPI_Sendrecv(v,  n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+           buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+                      ms->mpi_comm_masters, &mpi_req);
+            MPI_Recv(buf, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
+                     ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            v[i] = buf[i];
+        }
+        sfree(buf);
+    }
+}
+
+
+static void exchange_ints(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, int *v, int n)
+{
+    int *buf;
+    int  i;
+
+    if (v)
+    {
+        snew(buf, n);
+#ifdef GMX_MPI
+        /*
+           MPI_Sendrecv(v,  n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+             buf,n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
+             ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+                      ms->mpi_comm_masters, &mpi_req);
+            MPI_Recv(buf, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
+                     ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            v[i] = buf[i];
+        }
+        sfree(buf);
+    }
+}
+
+static void exchange_doubles(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, double *v, int n)
+{
+    double *buf;
+    int     i;
+
+    if (v)
+    {
+        snew(buf, n);
+#ifdef GMX_MPI
+        /*
+           MPI_Sendrecv(v,  n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+           buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+                      ms->mpi_comm_masters, &mpi_req);
+            MPI_Recv(buf, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
+                     ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            v[i] = buf[i];
+        }
+        sfree(buf);
+    }
+}
+
+static void exchange_rvecs(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, rvec *v, int n)
+{
+    rvec *buf;
+    int   i;
+
+    if (v)
+    {
+        snew(buf, n);
+#ifdef GMX_MPI
+        /*
+           MPI_Sendrecv(v[0],  n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+           buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mpi_comm_masters,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+                      ms->mpi_comm_masters, &mpi_req);
+            MPI_Recv(buf[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
+                     ms->mpi_comm_masters, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            copy_rvec(buf[i], v[i]);
+        }
+        sfree(buf);
+    }
+}
+
+static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+{
+    /* When t_state changes, this code should be updated. */
+    int ngtc, nnhpres;
+    ngtc    = state->ngtc * state->nhchainlength;
+    nnhpres = state->nnhpres* state->nhchainlength;
+    exchange_rvecs(ms, b, state->box, DIM);
+    exchange_rvecs(ms, b, state->box_rel, DIM);
+    exchange_rvecs(ms, b, state->boxv, DIM);
+    exchange_reals(ms, b, &(state->veta), 1);
+    exchange_reals(ms, b, &(state->vol0), 1);
+    exchange_rvecs(ms, b, state->svir_prev, DIM);
+    exchange_rvecs(ms, b, state->fvir_prev, DIM);
+    exchange_rvecs(ms, b, state->pres_prev, DIM);
+    exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
+    exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
+    exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
+    exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
+    exchange_doubles(ms, b, state->therm_integral, state->ngtc);
+    exchange_rvecs(ms, b, state->x, state->natoms);
+    exchange_rvecs(ms, b, state->v, state->natoms);
+    exchange_rvecs(ms, b, state->sd_X, state->natoms);
+}
+
+static void copy_rvecs(rvec *s, rvec *d, int n)
+{
+    int i;
+
+    if (d != NULL)
+    {
+        for (i = 0; i < n; i++)
+        {
+            copy_rvec(s[i], d[i]);
+        }
+    }
+}
+
+static void copy_doubles(const double *s, double *d, int n)
+{
+    int i;
+
+    if (d != NULL)
+    {
+        for (i = 0; i < n; i++)
+        {
+            d[i] = s[i];
+        }
+    }
+}
+
+static void copy_reals(const real *s, real *d, int n)
+{
+    int i;
+
+    if (d != NULL)
+    {
+        for (i = 0; i < n; i++)
+        {
+            d[i] = s[i];
+        }
+    }
+}
+
+static void copy_ints(const int *s, int *d, int n)
+{
+    int i;
+
+    if (d != NULL)
+    {
+        for (i = 0; i < n; i++)
+        {
+            d[i] = s[i];
+        }
+    }
+}
+
+#define scopy_rvecs(v, n)   copy_rvecs(state->v, state_local->v, n);
+#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
+#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
+#define scopy_ints(v, n)   copy_ints(state->v, state_local->v, n);
+
+static void copy_state_nonatomdata(t_state *state, t_state *state_local)
+{
+    /* When t_state changes, this code should be updated. */
+    int ngtc, nnhpres;
+    ngtc    = state->ngtc * state->nhchainlength;
+    nnhpres = state->nnhpres* state->nhchainlength;
+    scopy_rvecs(box, DIM);
+    scopy_rvecs(box_rel, DIM);
+    scopy_rvecs(boxv, DIM);
+    state_local->veta = state->veta;
+    state_local->vol0 = state->vol0;
+    scopy_rvecs(svir_prev, DIM);
+    scopy_rvecs(fvir_prev, DIM);
+    scopy_rvecs(pres_prev, DIM);
+    scopy_doubles(nosehoover_xi, ngtc);
+    scopy_doubles(nosehoover_vxi, ngtc);
+    scopy_doubles(nhpres_xi, nnhpres);
+    scopy_doubles(nhpres_vxi, nnhpres);
+    scopy_doubles(therm_integral, state->ngtc);
+    scopy_rvecs(x, state->natoms);
+    scopy_rvecs(v, state->natoms);
+    scopy_rvecs(sd_X, state->natoms);
+    copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
+    scopy_reals(lambda, efptNR);
+}
+
+static void scale_velocities(t_state *state, real fac)
+{
+    int i;
+
+    if (state->v)
+    {
+        for (i = 0; i < state->natoms; i++)
+        {
+            svmul(fac, state->v[i], state->v[i]);
+        }
+    }
+}
+
+static void print_transition_matrix(FILE *fplog, int n, int **nmoves, int *nattempt)
+{
+    int   i, j, ntot;
+    float Tprint;
+
+    ntot = nattempt[0] + nattempt[1];
+    fprintf(fplog, "\n");
+    fprintf(fplog, "Repl");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "    ");  /* put the title closer to the center */
+    }
+    fprintf(fplog, "Empirical Transition Matrix\n");
+
+    fprintf(fplog, "Repl");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%8d", (i+1));
+    }
+    fprintf(fplog, "\n");
+
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "Repl");
+        for (j = 0; j < n; j++)
+        {
+            Tprint = 0.0;
+            if (nmoves[i][j] > 0)
+            {
+                Tprint = nmoves[i][j]/(2.0*ntot);
+            }
+            fprintf(fplog, "%8.4f", Tprint);
+        }
+        fprintf(fplog, "%3d\n", i);
+    }
+}
+
+static void print_ind(FILE *fplog, const char *leg, int n, int *ind, gmx_bool *bEx)
+{
+    int i;
+
+    fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
+    for (i = 1; i < n; i++)
+    {
+        fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
+    }
+    fprintf(fplog, "\n");
+}
+
+static void print_allswitchind(FILE *fplog, int n, int *pind, int *allswaps, int *tmpswap)
+{
+    int i;
+
+    for (i = 0; i < n; i++)
+    {
+        tmpswap[i] = allswaps[i];
+    }
+    for (i = 0; i < n; i++)
+    {
+        allswaps[i] = tmpswap[pind[i]];
+    }
+
+    fprintf(fplog, "\nAccepted Exchanges:   ");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%d ", pind[i]);
+    }
+    fprintf(fplog, "\n");
+
+    /* the "Order After Exchange" is the state label corresponding to the configuration that
+       started in state listed in order, i.e.
+
+       3 0 1 2
+
+       means that the:
+       configuration starting in simulation 3 is now in simulation 0,
+       configuration starting in simulation 0 is now in simulation 1,
+       configuration starting in simulation 1 is now in simulation 2,
+       configuration starting in simulation 2 is now in simulation 3
+     */
+    fprintf(fplog, "Order After Exchange: ");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%d ", allswaps[i]);
+    }
+    fprintf(fplog, "\n\n");
+}
+
+static void print_prob(FILE *fplog, const char *leg, int n, real *prob)
+{
+    int  i;
+    char buf[8];
+
+    fprintf(fplog, "Repl %2s ", leg);
+    for (i = 1; i < n; i++)
+    {
+        if (prob[i] >= 0)
+        {
+            sprintf(buf, "%4.2f", prob[i]);
+            fprintf(fplog, "  %3s", buf[0] == '1' ? "1.0" : buf+1);
+        }
+        else
+        {
+            fprintf(fplog, "     ");
+        }
+    }
+    fprintf(fplog, "\n");
+}
+
+static void print_count(FILE *fplog, const char *leg, int n, int *count)
+{
+    int i;
+
+    fprintf(fplog, "Repl %2s ", leg);
+    for (i = 1; i < n; i++)
+    {
+        fprintf(fplog, " %4d", count[i]);
+    }
+    fprintf(fplog, "\n");
+}
+
+static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int a, int b, int ap, int bp)
+{
+
+    real   ediff, dpV, delta = 0;
+    real  *Epot = re->Epot;
+    real  *Vol  = re->Vol;
+    real **de   = re->de;
+    real  *beta = re->beta;
+
+    /* Two cases; we are permuted and not.  In all cases, setting ap = a and bp = b will reduce
+       to the non permuted case */
+
+    switch (re->type)
+    {
+        case ereTEMP:
+            /*
+             * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
+             */
+            ediff = Epot[b] - Epot[a];
+            delta = -(beta[bp] - beta[ap])*ediff;
+            break;
+        case ereLAMBDA:
+            /* two cases:  when we are permuted, and not.  */
+            /* non-permuted:
+               ediff =  E_new - E_old
+                     =  [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
+                     =  [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
+                     =  de[b][a] + de[a][b] */
+
+            /* permuted:
+               ediff =  E_new - E_old
+                     =  [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
+                     =  [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
+                     =  [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
+                     =  [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
+                     =  (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b])    */
+            /* but, in the current code implementation, we flip configurations, not indices . . .
+               So let's examine that.
+                     =  [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
+                     =  [H_b(x_ap) - H_a(x_ap)]  + [H_a(x_bp) - H_b(x_pb)]
+                     = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
+                     So, if we exchange b<=> bp and a<=> ap, we return to the same result.
+                     So the simple solution is to flip the
+                     position of perturbed and original indices in the tests.
+             */
+
+            ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
+            delta = ediff*beta[a]; /* assume all same temperature in this case */
+            break;
+        case ereTL:
+            /* not permuted:  */
+            /* delta =  reduced E_new - reduced E_old
+                     =  [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
+                     =  [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
+                     =  [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
+                        [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
+                     =  [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
+                        beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
+                     =  beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
+            /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
+            /* permuted (big breath!) */
+            /*   delta =  reduced E_new - reduced E_old
+                     =  [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
+                     =  [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+                     =  [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+                        - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
+                        - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+                     =  [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
+                        [(beta_ap H_ap(x_b)  - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
+             + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+                     =  [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
+                        [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
+             + beta_pb (H_a(x_a) - H_b(x_b))  - beta_ap (H_a(x_a) - H_b(x_b))
+                     =  ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b]  - beta_bp de[bp][b])
+             + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b))  */
+            delta = beta[bp]*(de[bp][a] - de[bp][b]) + beta[ap]*(de[ap][b] - de[ap][a]) - (beta[bp]-beta[ap])*(Epot[b]-Epot[a]);
+            break;
+        default:
+            gmx_incons("Unknown replica exchange quantity");
+    }
+    if (bPrint)
+    {
+        fprintf(fplog, "Repl %d <-> %d  dE_term = %10.3e (kT)\n", a, b, delta);
+    }
+    if (re->bNPT)
+    {
+        /* revist the calculation for 5.0.  Might be some improvements. */
+        dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
+        if (bPrint)
+        {
+            fprintf(fplog, "  dpV = %10.3e  d = %10.3e\n", dpV, delta + dpV);
+        }
+        delta += dpV;
+    }
+    return delta;
+}
+
+static void
+test_for_replica_exchange(FILE                 *fplog,
+                          const gmx_multisim_t *ms,
+                          struct gmx_repl_ex   *re,
+                          gmx_enerdata_t       *enerd,
+                          real                  vol,
+                          gmx_int64_t           step,
+                          real                  time)
+{
+    int       m, i, j, a, b, ap, bp, i0, i1, tmp;
+    real      ediff = 0, delta = 0, dpV = 0;
+    gmx_bool  bPrint, bMultiEx;
+    gmx_bool *bEx      = re->bEx;
+    real     *prob     = re->prob;
+    int      *pind     = re->destinations; /* permuted index */
+    gmx_bool  bEpot    = FALSE;
+    gmx_bool  bDLambda = FALSE;
+    gmx_bool  bVol     = FALSE;
+    gmx_rng_t rng;
+
+    bMultiEx = (re->nex > 1);  /* multiple exchanges at each state */
+    fprintf(fplog, "Replica exchange at step " "%"GMX_PRId64 " time %.5f\n", step, time);
+
+    if (re->bNPT)
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->Vol[i] = 0;
+        }
+        bVol               = TRUE;
+        re->Vol[re->repl]  = vol;
+    }
+    if ((re->type == ereTEMP || re->type == ereTL))
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->Epot[i] = 0;
+        }
+        bEpot              = TRUE;
+        re->Epot[re->repl] = enerd->term[F_EPOT];
+        /* temperatures of different states*/
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ);
+        }
+    }
+    else
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->beta[i] = 1.0/(re->temp*BOLTZ);  /* we have a single temperature */
+        }
+    }
+    if (re->type == ereLAMBDA || re->type == ereTL)
+    {
+        bDLambda = TRUE;
+        /* lambda differences. */
+        /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
+           minus the energy of the jth simulation in the jth Hamiltonian */
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = 0; j < re->nrepl; j++)
+            {
+                re->de[i][j] = 0;
+            }
+        }
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);
+        }
+    }
+
+    /* now actually do the communication */
+    if (bVol)
+    {
+        gmx_sum_sim(re->nrepl, re->Vol, ms);
+    }
+    if (bEpot)
+    {
+        gmx_sum_sim(re->nrepl, re->Epot, ms);
+    }
+    if (bDLambda)
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            gmx_sum_sim(re->nrepl, re->de[i], ms);
+        }
+    }
+
+    /* make a duplicate set of indices for shuffling */
+    for (i = 0; i < re->nrepl; i++)
+    {
+        pind[i] = re->ind[i];
+    }
+
+    if (bMultiEx)
+    {
+        /* multiple random switch exchange */
+        int nself = 0;
+        for (i = 0; i < re->nex + nself; i++)
+        {
+            double rnd[2];
+
+            gmx_rng_cycle_2uniform(step, i*2, re->seed, RND_SEED_REPLEX, rnd);
+            /* randomly select a pair  */
+            /* in theory, could reduce this by identifying only which switches had a nonneglibible
+               probability of occurring (log p > -100) and only operate on those switches */
+            /* find out which state it is from, and what label that state currently has. Likely
+               more work that useful. */
+            i0 = (int)(re->nrepl*rnd[0]);
+            i1 = (int)(re->nrepl*rnd[1]);
+            if (i0 == i1)
+            {
+                nself++;
+                continue;  /* self-exchange, back up and do it again */
+            }
+
+            a  = re->ind[i0]; /* what are the indices of these states? */
+            b  = re->ind[i1];
+            ap = pind[i0];
+            bp = pind[i1];
+
+            bPrint = FALSE; /* too noisy */
+            /* calculate the energy difference */
+            /* if the code changes to flip the STATES, rather than the configurations,
+               use the commented version of the code */
+            /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
+            delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
+
+            /* we actually only use the first space in the prob and bEx array,
+               since there are actually many switches between pairs. */
+
+            if (delta <= 0)
+            {
+                /* accepted */
+                prob[0] = 1;
+                bEx[0]  = TRUE;
+            }
+            else
+            {
+                if (delta > PROBABILITYCUTOFF)
+                {
+                    prob[0] = 0;
+                }
+                else
+                {
+                    prob[0] = exp(-delta);
+                }
+                /* roll a number to determine if accepted */
+                gmx_rng_cycle_2uniform(step, i*2+1, re->seed, RND_SEED_REPLEX, rnd);
+                bEx[0] = rnd[0] < prob[0];
+            }
+            re->prob_sum[0] += prob[0];
+
+            if (bEx[0])
+            {
+                /* swap the states */
+                tmp      = pind[i0];
+                pind[i0] = pind[i1];
+                pind[i1] = tmp;
+            }
+        }
+        re->nattempt[0]++;  /* keep track of total permutation trials here */
+        print_allswitchind(fplog, re->nrepl, pind, re->allswaps, re->tmpswap);
+    }
+    else
+    {
+        /* standard nearest neighbor replica exchange */
+
+        m = (step / re->nst) % 2;
+        for (i = 1; i < re->nrepl; i++)
+        {
+            a = re->ind[i-1];
+            b = re->ind[i];
+
+            bPrint = (re->repl == a || re->repl == b);
+            if (i % 2 == m)
+            {
+                delta = calc_delta(fplog, bPrint, re, a, b, a, b);
+                if (delta <= 0)
+                {
+                    /* accepted */
+                    prob[i] = 1;
+                    bEx[i]  = TRUE;
+                }
+                else
+                {
+                    double rnd[2];
+
+                    if (delta > PROBABILITYCUTOFF)
+                    {
+                        prob[i] = 0;
+                    }
+                    else
+                    {
+                        prob[i] = exp(-delta);
+                    }
+                    /* roll a number to determine if accepted */
+                    gmx_rng_cycle_2uniform(step, i, re->seed, RND_SEED_REPLEX, rnd);
+                    bEx[i] = rnd[0] < prob[i];
+                }
+                re->prob_sum[i] += prob[i];
+
+                if (bEx[i])
+                {
+                    /* swap these two */
+                    tmp       = pind[i-1];
+                    pind[i-1] = pind[i];
+                    pind[i]   = tmp;
+                    re->nexchange[i]++;  /* statistics for back compatibility */
+                }
+            }
+            else
+            {
+                prob[i] = -1;
+                bEx[i]  = FALSE;
+            }
+        }
+        /* print some statistics */
+        print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
+        print_prob(fplog, "pr", re->nrepl, prob);
+        fprintf(fplog, "\n");
+        re->nattempt[m]++;
+    }
+
+    /* record which moves were made and accepted */
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->nmoves[re->ind[i]][pind[i]] += 1;
+        re->nmoves[pind[i]][re->ind[i]] += 1;
+    }
+    fflush(fplog); /* make sure we can see what the last exchange was */
+}
+
+static void write_debug_x(t_state *state)
+{
+    int i;
+
+    if (debug)
+    {
+        for (i = 0; i < state->natoms; i += 10)
+        {
+            fprintf(debug, "dx %5d %10.5f %10.5f %10.5f\n", i, state->x[i][XX], state->x[i][YY], state->x[i][ZZ]);
+        }
+    }
+}
+
+static void
+cyclic_decomposition(const int *destinations,
+                     int      **cyclic,
+                     gmx_bool  *incycle,
+                     const int  nrepl,
+                     int       *nswap)
+{
+
+    int i, j, c, p;
+    int maxlen = 1;
+    for (i = 0; i < nrepl; i++)
+    {
+        incycle[i] = FALSE;
+    }
+    for (i = 0; i < nrepl; i++)  /* one cycle for each replica */
+    {
+        if (incycle[i])
+        {
+            cyclic[i][0] = -1;
+            continue;
+        }
+        cyclic[i][0] = i;
+        incycle[i]   = TRUE;
+        c            = 1;
+        p            = i;
+        for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
+        {
+            p = destinations[p];    /* start permuting */
+            if (p == i)
+            {
+                cyclic[i][c] = -1;
+                if (c > maxlen)
+                {
+                    maxlen = c;
+                }
+                break; /* we've reached the original element, the cycle is complete, and we marked the end. */
+            }
+            else
+            {
+                cyclic[i][c] = p;  /* each permutation gives a new member of the cycle */
+                incycle[p]   = TRUE;
+                c++;
+            }
+        }
+    }
+    *nswap = maxlen - 1;
+
+    if (debug)
+    {
+        for (i = 0; i < nrepl; i++)
+        {
+            fprintf(debug, "Cycle %d:", i);
+            for (j = 0; j < nrepl; j++)
+            {
+                if (cyclic[i][j] < 0)
+                {
+                    break;
+                }
+                fprintf(debug, "%2d", cyclic[i][j]);
+            }
+            fprintf(debug, "\n");
+        }
+        fflush(debug);
+    }
+}
+
+static void
+compute_exchange_order(FILE     *fplog,
+                       int     **cyclic,
+                       int     **order,
+                       const int nrepl,
+                       const int maxswap)
+{
+    int i, j;
+
+    for (j = 0; j < maxswap; j++)
+    {
+        for (i = 0; i < nrepl; i++)
+        {
+            if (cyclic[i][j+1] >= 0)
+            {
+                order[cyclic[i][j+1]][j] = cyclic[i][j];
+                order[cyclic[i][j]][j]   = cyclic[i][j+1];
+            }
+        }
+        for (i = 0; i < nrepl; i++)
+        {
+            if (order[i][j] < 0)
+            {
+                order[i][j] = i; /* if it's not exchanging, it should stay this round*/
+            }
+        }
+    }
+
+    if (debug)
+    {
+        fprintf(fplog, "Replica Exchange Order\n");
+        for (i = 0; i < nrepl; i++)
+        {
+            fprintf(fplog, "Replica %d:", i);
+            for (j = 0; j < maxswap; j++)
+            {
+                if (order[i][j] < 0)
+                {
+                    break;
+                }
+                fprintf(debug, "%2d", order[i][j]);
+            }
+            fprintf(fplog, "\n");
+        }
+        fflush(fplog);
+    }
+}
+
+static void
+prepare_to_do_exchange(FILE               *fplog,
+                       struct gmx_repl_ex *re,
+                       const int           replica_id,
+                       int                *maxswap,
+                       gmx_bool           *bThisReplicaExchanged)
+{
+    int i, j;
+    /* Hold the cyclic decomposition of the (multiple) replica
+     * exchange. */
+    gmx_bool bAnyReplicaExchanged = FALSE;
+    *bThisReplicaExchanged = FALSE;
+
+    for (i = 0; i < re->nrepl; i++)
+    {
+        if (re->destinations[i] != re->ind[i])
+        {
+            /* only mark as exchanged if the index has been shuffled */
+            bAnyReplicaExchanged = TRUE;
+            break;
+        }
+    }
+    if (bAnyReplicaExchanged)
+    {
+        /* reinitialize the placeholder arrays */
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = 0; j < re->nrepl; j++)
+            {
+                re->cyclic[i][j] = -1;
+                re->order[i][j]  = -1;
+            }
+        }
+
+        /* Identify the cyclic decomposition of the permutation (very
+         * fast if neighbor replica exchange). */
+        cyclic_decomposition(re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
+
+        /* Now translate the decomposition into a replica exchange
+         * order at each step. */
+        compute_exchange_order(fplog, re->cyclic, re->order, re->nrepl, *maxswap);
+
+        /* Did this replica do any exchange at any point? */
+        for (j = 0; j < *maxswap; j++)
+        {
+            if (replica_id != re->order[replica_id][j])
+            {
+                *bThisReplicaExchanged = TRUE;
+                break;
+            }
+        }
+    }
+}
+
+gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *re,
+                          t_state *state, gmx_enerdata_t *enerd,
+                          t_state *state_local, gmx_int64_t step, real time)
+{
+    int i, j;
+    int replica_id = 0;
+    int exchange_partner;
+    int maxswap = 0;
+    /* Number of rounds of exchanges needed to deal with any multiple
+     * exchanges. */
+    /* Where each replica ends up after the exchange attempt(s). */
+    /* The order in which multiple exchanges will occur. */
+    gmx_bool bThisReplicaExchanged = FALSE;
+
+    if (MASTER(cr))
+    {
+        replica_id  = re->repl;
+        test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
+        prepare_to_do_exchange(fplog, re, replica_id, &maxswap, &bThisReplicaExchanged);
+    }
+    /* Do intra-simulation broadcast so all processors belonging to
+     * each simulation know whether they need to participate in
+     * collecting the state. Otherwise, they might as well get on with
+     * the next thing to do. */
+    if (DOMAINDECOMP(cr))
+    {
+#ifdef GMX_MPI
+        MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr),
+                  cr->mpi_comm_mygroup);
+#endif
+    }
+
+    if (bThisReplicaExchanged)
+    {
+        /* Exchange the states */
+        /* Collect the global state on the master node */
+        if (DOMAINDECOMP(cr))
+        {
+            dd_collect_state(cr->dd, state_local, state);
+        }
+        else
+        {
+            copy_state_nonatomdata(state_local, state);
+        }
+
+        if (MASTER(cr))
+        {
+            /* There will be only one swap cycle with standard replica
+             * exchange, but there may be multiple swap cycles if we
+             * allow multiple swaps. */
+
+            for (j = 0; j < maxswap; j++)
+            {
+                exchange_partner = re->order[replica_id][j];
+
+                if (exchange_partner != replica_id)
+                {
+                    /* Exchange the global states between the master nodes */
+                    if (debug)
+                    {
+                        fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
+                    }
+                    exchange_state(cr->ms, exchange_partner, state);
+                }
+            }
+            /* For temperature-type replica exchange, we need to scale
+             * the velocities. */
+            if (re->type == ereTEMP || re->type == ereTL)
+            {
+                scale_velocities(state, sqrt(re->q[ereTEMP][replica_id]/re->q[ereTEMP][re->destinations[replica_id]]));
+            }
+
+        }
+
+        /* With domain decomposition the global state is distributed later */
+        if (!DOMAINDECOMP(cr))
+        {
+            /* Copy the global state to the local state data structure */
+            copy_state_nonatomdata(state, state_local);
+        }
+    }
+
+    return bThisReplicaExchanged;
+}
+
+void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
+{
+    int  i;
+
+    fprintf(fplog, "\nReplica exchange statistics\n");
+
+    if (re->nex == 0)
+    {
+        fprintf(fplog, "Repl  %d attempts, %d odd, %d even\n",
+                re->nattempt[0]+re->nattempt[1], re->nattempt[1], re->nattempt[0]);
+
+        fprintf(fplog, "Repl  average probabilities:\n");
+        for (i = 1; i < re->nrepl; i++)
+        {
+            if (re->nattempt[i%2] == 0)
+            {
+                re->prob[i] = 0;
+            }
+            else
+            {
+                re->prob[i] =  re->prob_sum[i]/re->nattempt[i%2];
+            }
+        }
+        print_ind(fplog, "", re->nrepl, re->ind, NULL);
+        print_prob(fplog, "", re->nrepl, re->prob);
+
+        fprintf(fplog, "Repl  number of exchanges:\n");
+        print_ind(fplog, "", re->nrepl, re->ind, NULL);
+        print_count(fplog, "", re->nrepl, re->nexchange);
+
+        fprintf(fplog, "Repl  average number of exchanges:\n");
+        for (i = 1; i < re->nrepl; i++)
+        {
+            if (re->nattempt[i%2] == 0)
+            {
+                re->prob[i] = 0;
+            }
+            else
+            {
+                re->prob[i] =  ((real)re->nexchange[i])/re->nattempt[i%2];
+            }
+        }
+        print_ind(fplog, "", re->nrepl, re->ind, NULL);
+        print_prob(fplog, "", re->nrepl, re->prob);
+
+        fprintf(fplog, "\n");
+    }
+    /* print the transition matrix */
+    print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
+}
