diff --git a/README-versions.md b/README-versions.md
index 4c845aaa3..c9ed19665 100644
--- a/README-versions.md
+++ b/README-versions.md
@@ -1,12 +1,21 @@
+[Versions included in GROMACS](#versions-included-in-GROMACS)
+
 [Versions included in LAMMPS](#versions-included-in-LAMMPS)
 
 [Versions included in NAMD](#versions-included-in-NAMD)
 
 [Versions included in VMD](#versions-included-in-VMD)
 
+### Versions included in GROMACS
+GROMACS version | Colvars version
+-------------- | ---------------
+2024 | [2023-12-05](https://github.com/Colvars/colvars/tree/gromacs-2024)
+
 ### Versions included in LAMMPS
 LAMMPS version | Colvars version
 -------------- | ---------------
+stable_29Aug2024 | [2024-06-04](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Aug2024)
+stable_2Aug2023 | [2023-05-01](https://github.com/Colvars/colvars/releases/tag/lammps-stable_2Aug2023)
 stable_23Jun2022 | [2022-05-24](https://github.com/Colvars/colvars/releases/tag/lammps-stable_23Jun2022)
 stable_29Sep2021 | [2021-09-13](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Sep2021)
 stable_29Oct2020 | [2020-09-17](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Oct2020)
@@ -27,6 +36,7 @@ stable_4Nov2016 | [2016-10-21](https://github.com/Colvars/colvars/releases/tag/l
 
 NAMD version | Colvars version
 -------------- | ---------------
+3.0 | [2024-06-04](https://github.com/Colvars/colvars/tree/namd-3.0)
 2.14 | [2020-07-07](https://github.com/Colvars/colvars/releases/tag/namd-2.14)
 2.13b2 | [2018-10-12](https://github.com/Colvars/colvars/releases/tag/namd-2.13b2)
 2.13b1 | [2018-09-07](https://github.com/Colvars/colvars/releases/tag/namd-2.13b1)
@@ -40,6 +50,7 @@ VMD version | Colvars version
 -------------- | ---------------
 1.9.4a58 | [2022-04-14](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a58)
 1.9.4a49 | [2020-10-22](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a49)
+1.9.4a12 | [2017-10-11](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a12)
 1.9.3 | [2016-10-26](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.3)
 1.9.2 | [2014-10-13](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.2)
 
diff --git a/README.md b/README.md
index cf8f8ed3d..874d278c4 100644
--- a/README.md
+++ b/README.md
@@ -110,7 +110,7 @@ All of the above MD engine versions are automatically tested as part of GitHub A
 
 ## Legacy GROMACS-Colvars patched releases
 
-Versions GROMACS prior to 2024 are supported through the use of a customized `mdrun` command line; source code of these patched releases is available [here](https://github.com/Colvars/gromacs).  When posting a message to the [Gromacs forum](https://gromacs.bioexcel.eu/) regarding the use of these patched releases, please specify "GROMACS modification: **Yes**".
+Versions GROMACS prior to 2024 are no longer supported by the current version of Colvars: please use GROMACS 2024 or later.
 
 
 ## Which version of Colvars is recommended?
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 3162bf8dc..7ae06cc9e 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -90,6 +90,25 @@ endif()
 
 include(buildColvarsLepton)
 
+
+option(COLVARS_MPI "Link against a MPI library" OFF)
+
+if(COLVARS_MPI)
+  find_package(MPI)
+  if(${MPI_FOUND})
+    include_directories(SYSTEM ${MPI_CXX_INCLUDE_PATH})
+    target_compile_options(colvars PRIVATE -DCOLVARS_MPI)
+    add_compile_options(-DCOLVARS_MPI)
+    target_link_libraries(colvars ${MPI_CXX_LIBRARIES})
+    set(COLVARS_MPI ON)
+  else()
+    if(NOT ${MPI_FOUND})
+      message(FATAL_ERROR "MPI not found.")
+    endif()
+  endif()
+endif()
+
+
 option(COLVARS_TCL "Link against the Tcl library" OFF)
 
 if(COLVARS_TCL)
diff --git a/doc/Makefile b/doc/Makefile
index c78c7a1cc..4b16c2ae3 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,6 +1,6 @@
 .PHONY: all pdf html doxygen webpage webpage-legacy images \
 	install clean clean-all \
-	update-code-refs update-cvscript-cmdline-doc updates
+	update-code-refs update-cvscript-cmdline-doc updates update-version-list
 
 ifeq ($(COLVARS_RELEASE),)
 # Unless defined otherwise, the release label is the name of the branch
@@ -90,7 +90,7 @@ clean-all: clean
 	@echo
 	@echo "Note: only removed files that this branch is set to build."
 
-version-list:
+update-version-list:
 	./print_engine_versions.sh > ../README-versions.md
 
 update-code-refs:
diff --git a/doc/cv_version.tex b/doc/cv_version.tex
index c89f44592..1adc138b4 100644
--- a/doc/cv_version.tex
+++ b/doc/cv_version.tex
@@ -1 +1 @@
-\newcommand{\cvversion}{2024-09-17}
+\newcommand{\cvversion}{2024-10-05}
diff --git a/doc/print_engine_versions.sh b/doc/print_engine_versions.sh
index b4df3529f..39510d36f 100755
--- a/doc/print_engine_versions.sh
+++ b/doc/print_engine_versions.sh
@@ -1,6 +1,12 @@
 #!/bin/bash
 
-source ../devel-tools/version_functions.sh
+TOPDIR=$(git rev-parse --show-toplevel)
+if [ ! -d ${TOPDIR} ] ; then
+  echo "Error: cannot identify top project directory." >& 2
+  exit 1
+fi
+
+source ${TOPDIR}/devel-tools/version_functions.sh
 
 
 reformat_lammps_version() {
@@ -18,20 +24,32 @@ print_tag_versions() {
     local tag
     local colvars_version
     local lammps_version=""
-    for tag in $(git tag -l|grep ^${tag_prefix}); do
+
+    for tag in $(git tag -l | grep ^${tag_prefix}) ; do
         local package_version=${tag#${tag_prefix}}
         colvars_version=$(get_colvarmodule_version ${tag})
-        if [ ${package} = LAMMPS ] ; then
+        if [ ${package} == LAMMPS ] ; then
             lammps_version=$(reformat_lammps_version ${package_version#*_})" "
         fi
         echo "${lammps_version}${package_version} | [${colvars_version}](https://github.com/Colvars/colvars/releases/tag/${tag})"
     done
+
+    for branch in $(git branch -l --format='%(refname)' | sed -s 's/refs\/heads\///' | grep ^${tag_prefix}) ; do
+        local package_version=${branch#${tag_prefix}}
+        colvars_version=$(get_colvarmodule_version ${branch})
+        if [ ${package} == LAMMPS ] ; then
+            lammps_version=$(reformat_lammps_version ${package_version#*_})" "
+        fi
+        if [ ${package} == GROMACS ] ; then
+            if [ ${branch} == gromacs-2023 ] || [ ${branch} == gromacs-2022 ] ; then
+                # These branches do not reflect GROMACS standard releases
+                continue
+            fi
+        fi
+        echo "${lammps_version}${package_version} | [${colvars_version}](https://github.com/Colvars/colvars/tree/${branch})"
+    done
 }
 
-for package in LAMMPS NAMD VMD ; do
-    echo "[Versions included in ${package}](#versions-included-in-${package})"
-    echo
-done
 
 sort_versions(){
     sort -r
@@ -43,18 +61,24 @@ sort_lammps_versions(){
 }
 
 
-for package in LAMMPS NAMD VMD ; do
+for package in GROMACS LAMMPS NAMD VMD ; do
+    echo "[Versions included in ${package}](#versions-included-in-${package})"
+    echo
+done
+
+
+for package in GROMACS LAMMPS NAMD VMD ; do
     echo "### Versions included in ${package}"
-    if [ ${package} = NAMD ] ; then
+    if [ ${package} == NAMD ] ; then
         echo "(Note: the Colvars version included in NAMD 2.12 is the same as the one included in 2.12b1 with only bugfixes applied: therefore, NAMD 2.12 does not correspond to a specific version of the Colvars source tree)"
         echo
     fi
     echo "${package} version | Colvars version"
     echo "-------------- | ---------------"
     sort_command=sort_versions
-    if [ ${package} = LAMMPS ] ; then
+    if [ ${package} == LAMMPS ] ; then
         sort_command=sort_lammps_versions
     fi
-    print_tag_versions ${package} $(echo ${package}- | tr '[:upper:]' '[:lower:]') | ${sort_command}
+    print_tag_versions ${package} ${package,,}- | ${sort_command}
     echo
 done
diff --git a/gromacs/gromacs-mdmodules/.clang-format b/gromacs/.clang-format
similarity index 100%
rename from gromacs/gromacs-mdmodules/.clang-format
rename to gromacs/.clang-format
diff --git a/gromacs/gromacs-mdmodules/CMakeLists.txt.Lepton.diff b/gromacs/CMakeLists.txt.Lepton.diff
similarity index 100%
rename from gromacs/gromacs-mdmodules/CMakeLists.txt.Lepton.diff
rename to gromacs/CMakeLists.txt.Lepton.diff
diff --git a/gromacs/CMakeLists.txt.diff b/gromacs/CMakeLists.txt.diff
index bcfa2b1dc..e69de29bb 100644
--- a/gromacs/CMakeLists.txt.diff
+++ b/gromacs/CMakeLists.txt.diff
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 70b0369bed..cccfe2aa1b 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -678,6 +678,8 @@ include(gmxManageLmfit)
- 
- include(gmxManageMuparser)
- 
-+include(gmxManageLepton)
-+
- include(gmxManageColvars)
- 
- ##################################################
diff --git a/gromacs/cmake/gmxManageColvars.cmake b/gromacs/cmake/gmxManageColvars.cmake
index 3cd697075..509d56e11 100644
--- a/gromacs/cmake/gmxManageColvars.cmake
+++ b/gromacs/cmake/gmxManageColvars.cmake
@@ -38,25 +38,25 @@ gmx_option_multichoice(GMX_USE_COLVARS
     INTERNAL NONE)
 mark_as_advanced(GMX_USE_COLVARS)
 
-function(gmx_set_colvars_torch)
-  find_package(Torch)
-  if (Torch_FOUND)
-    message(STATUS "Torch found, enabling for Colvars")
-    set_property(TARGET colvars_objlib PROPERTY CXX_STANDARD 17)
-    target_compile_definitions(colvars_objlib PRIVATE -DTORCH)
-    target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
-    target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
-    target_link_libraries(libgromacs PRIVATE "${TORCH_LIBRARIES}")
-  endif()
-endfunction()
-
-
 function(gmx_manage_colvars)
     if(GMX_USE_COLVARS STREQUAL "INTERNAL")
+
         # Create an object library for the colvars sources
         set(COLVARS_DIR "${CMAKE_SOURCE_DIR}/src/external/colvars")
         file(GLOB COLVARS_SOURCES ${COLVARS_DIR}/*.cpp)
         add_library(colvars_objlib OBJECT ${COLVARS_SOURCES})
+        if(GMX_LIB_MPI)
+            target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_MPI)
+        endif()
+        if(GMX_OPENMP)
+            target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
+        endif()
+        if(GMX_TORCH)
+            target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
+            target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
+            target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_TORCH)
+        endif()
+
         # Set correctly the value of __cplusplus, which MSVC doesn't do by default
         target_compile_options(colvars_objlib PRIVATE $<$<CXX_COMPILER_ID:MSVC>:/Zc:__cplusplus>)
         # Ensure that colvars_objlib can be used in both STATIC and SHARED libraries.
@@ -66,10 +66,11 @@ function(gmx_manage_colvars)
         add_library(colvars INTERFACE)
         target_sources(colvars INTERFACE $<TARGET_OBJECTS:colvars_objlib>)
         target_include_directories(colvars SYSTEM INTERFACE $<BUILD_INTERFACE:${COLVARS_DIR}>)
-
-        if(GMX_OPENMP)
-            target_compile_options(colvars_objlib PRIVATE ${OpenMP_CXX_FLAGS})
-            target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
+        if(GMX_LIB_MPI)
+            target_compile_definitions(colvars INTERFACE -DCOLVARS_MPI)
+        endif()
+        if(GMX_TORCH)
+            target_compile_definitions(colvars INTERFACE -DCOLVARS_TORCH)
         endif()
 
         set(GMX_HAVE_COLVARS 1 CACHE INTERNAL "Is colvars found?")
@@ -81,7 +82,5 @@ function(gmx_manage_colvars)
 
         set(GMX_HAVE_COLVARS 0 CACHE INTERNAL "Is colvars found?")
     endif()
-
-    gmx_set_colvars_torch()
     mark_as_advanced(GMX_HAVE_COLVARS)
 endfunction()
diff --git a/gromacs/gmxManageColvars.cmake.diff b/gromacs/gmxManageColvars.cmake.diff
new file mode 100644
index 000000000..e69de29bb
diff --git a/gromacs/gromacs-mdmodules.patch b/gromacs/gromacs-mdmodules.patch
new file mode 100644
index 000000000..e69de29bb
diff --git a/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff b/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff
deleted file mode 100644
index 8b1378917..000000000
--- a/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt b/gromacs/src/applied_forces/colvars/CMakeLists.txt
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt
rename to gromacs/src/applied_forces/colvars/CMakeLists.txt
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp b/gromacs/src/applied_forces/colvars/colvarproxygromacs.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp
rename to gromacs/src/applied_forces/colvars/colvarproxygromacs.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h b/gromacs/src/applied_forces/colvars/colvarproxygromacs.h
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h
rename to gromacs/src/applied_forces/colvars/colvarproxygromacs.h
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp b/gromacs/src/applied_forces/colvars/colvarsMDModule.cpp
similarity index 96%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp
rename to gromacs/src/applied_forces/colvars/colvarsMDModule.cpp
index 8d0625289..ad876b602 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp
+++ b/gromacs/src/applied_forces/colvars/colvarsMDModule.cpp
@@ -49,6 +49,7 @@
 #include "gromacs/domdec/localatomsetmanager.h"
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/mdrunutility/mdmodulesnotifiers.h"
+#include "gromacs/mdrunutility/multisim.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/iforceprovider.h"
 #include "gromacs/mdtypes/imdmodule.h"
@@ -97,7 +98,7 @@ class ColvarsMDModule final : public IMDModule
      *     KeyValueTreeObjectBuilder as parameter
      *   - Acess topology using gmx_mtop_t notification
      *   - Access MDLogger for notifications output
-     *   - Access warninp for for grompp warnings output
+     *   - Access warning for for grompp warnings output
      *   - Coordinates, PBC and box for setting up the proxy
      */
     void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifier) override
@@ -192,6 +193,12 @@ class ColvarsMDModule final : public IMDModule
         };
         notifier->simulationSetupNotifier_.subscribe(setCommFunction);
 
+        // Retrieve the Multisim Record during simulations setup
+        const auto setMultisimFunction = [this](const gmx_multisim_t* ms) {
+            this->ColvarsSimulationsParameters_.setMultisim(ms);
+        };
+        notifier->simulationSetupNotifier_.subscribe(setMultisimFunction);
+
         // setting the simulation time step
         const auto setSimulationTimeStepFunction = [this](const SimulationTimeStep& simulationTimeStep) {
             this->ColvarsSimulationsParameters_.setSimulationTimeStep(simulationTimeStep.delta_t);
@@ -251,6 +258,7 @@ class ColvarsMDModule final : public IMDModule
                     colvarsOptions_.colvarsSeed(),
                     ColvarsSimulationsParameters_.localAtomSetManager(),
                     ColvarsSimulationsParameters_.comm(),
+                    ColvarsSimulationsParameters_.ms(),
                     ColvarsSimulationsParameters_.simulationTimeStep(),
                     colvarsOptions_.colvarsAtomCoords(),
                     colvarsOptions_.colvarsOutputPrefix(),
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h b/gromacs/src/applied_forces/colvars/colvarsMDModule.h
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.h
rename to gromacs/src/applied_forces/colvars/colvarsMDModule.h
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule_stub.cpp b/gromacs/src/applied_forces/colvars/colvarsMDModule_stub.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule_stub.cpp
rename to gromacs/src/applied_forces/colvars/colvarsMDModule_stub.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp b/gromacs/src/applied_forces/colvars/colvarsforceprovider.cpp
similarity index 97%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp
rename to gromacs/src/applied_forces/colvars/colvarsforceprovider.cpp
index be8434572..6b94d9a43 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp
+++ b/gromacs/src/applied_forces/colvars/colvarsforceprovider.cpp
@@ -57,6 +57,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdrunutility/multisim.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/forceoutput.h"
@@ -65,6 +66,7 @@
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/keyvaluetree.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 #include "gromacs/utility/smalloc.h"
@@ -173,6 +175,7 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfigStrin
                                            int                              seed,
                                            LocalAtomSetManager*             localAtomSetManager,
                                            const t_commrec*                 cr,
+                                           const gmx_multisim_t*            ms,
                                            double                           simulationTimeStep,
                                            const std::vector<RVec>&         colvarsCoords,
                                            const std::string&               outputPrefix,
@@ -236,6 +239,17 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfigStrin
     snew(fColvars, nColvarsAtoms);
     snew(xColvarsOldWhole, nColvarsAtoms);
 
+#if GMX_MPI
+    if (MAIN(cr))
+    {
+        if (isMultiSim(ms))
+        {
+            colvarproxy::set_replicas_mpi_communicator(ms->mainRanksComm_);
+        }
+    }
+#else
+    GMX_UNUSED_VALUE(ms);
+#endif
 
     // Check state status (did we read a cpt file?)
     if (MAIN(cr))
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h b/gromacs/src/applied_forces/colvars/colvarsforceprovider.h
similarity index 98%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h
rename to gromacs/src/applied_forces/colvars/colvarsforceprovider.h
index eb7666cba..028c17764 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h
+++ b/gromacs/src/applied_forces/colvars/colvarsforceprovider.h
@@ -61,6 +61,7 @@
 
 enum class PbcType : int;
 struct t_commrec;
+struct gmx_multisim_t;
 
 
 namespace gmx
@@ -182,6 +183,7 @@ class ColvarsForceProvider final : public ColvarProxyGromacs, public IForceProvi
      * \param[in] seed The colvars seed for random number generator
      * \param[in] localAtomSetManager Atom Manager to retrieve Colvars index atoms
      * \param[in] cr Communication Record
+     * \param[in] ms Multi-simulation record
      * \param[in] simulationTimeStep The simulation time step
      * \param[in] colvarsCoords The colvars atoms coordinates retrived from the TPR's KVT
      * \param[in] outputPrefix The prefix for output colvars files
@@ -196,6 +198,7 @@ class ColvarsForceProvider final : public ColvarProxyGromacs, public IForceProvi
                          int                                       seed,
                          LocalAtomSetManager*                      localAtomSetManager,
                          const t_commrec*                          cr,
+                         const gmx_multisim_t*                     ms,
                          double                                    simulationTimeStep,
                          const std::vector<RVec>&                  colvarsCoords,
                          const std::string&                        outputPrefix,
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp b/gromacs/src/applied_forces/colvars/colvarsoptions.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp
rename to gromacs/src/applied_forces/colvars/colvarsoptions.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h b/gromacs/src/applied_forces/colvars/colvarsoptions.h
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h
rename to gromacs/src/applied_forces/colvars/colvarsoptions.h
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp b/gromacs/src/applied_forces/colvars/colvarspreprocessor.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.cpp
rename to gromacs/src/applied_forces/colvars/colvarspreprocessor.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h b/gromacs/src/applied_forces/colvars/colvarspreprocessor.h
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarspreprocessor.h
rename to gromacs/src/applied_forces/colvars/colvarspreprocessor.h
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp b/gromacs/src/applied_forces/colvars/colvarssimulationsparameters.cpp
similarity index 95%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp
rename to gromacs/src/applied_forces/colvars/colvarssimulationsparameters.cpp
index f0e5e825a..52ec1a104 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp
+++ b/gromacs/src/applied_forces/colvars/colvarssimulationsparameters.cpp
@@ -114,6 +114,16 @@ const t_commrec* ColvarsSimulationsParameters::comm() const
     return cr_;
 }
 
+void ColvarsSimulationsParameters::setMultisim(const gmx_multisim_t* ms)
+{
+    ms_ = ms;
+}
+
+const gmx_multisim_t* ColvarsSimulationsParameters::ms() const
+{
+    return ms_;
+}
+
 
 void ColvarsSimulationsParameters::setLogger(const MDLogger& logger)
 {
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h b/gromacs/src/applied_forces/colvars/colvarssimulationsparameters.h
similarity index 94%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h
rename to gromacs/src/applied_forces/colvars/colvarssimulationsparameters.h
index 8d6a227d7..8ae9823b0 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.h
+++ b/gromacs/src/applied_forces/colvars/colvarssimulationsparameters.h
@@ -50,6 +50,7 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/logger.h"
+struct gmx_multisim_t;
 
 struct gmx_mtop_t;
 
@@ -109,7 +110,12 @@ class ColvarsSimulationsParameters
     //! Return the communicator
     const t_commrec* comm() const;
 
-    /*! \brief Set the logger for QMMM during mdrun
+    //! Set the Multisim record
+    void setMultisim(const gmx_multisim_t* ms);
+    //! Return Multisim record
+    const gmx_multisim_t* ms() const;
+
+    /*! \brief Set the logger for Colvars during mdrun
      * \param[in] logger Logger instance to be used for output
      */
     void setLogger(const MDLogger& logger);
@@ -128,6 +134,8 @@ class ColvarsSimulationsParameters
     t_atoms gmxAtoms_;
     //! The communicator
     const t_commrec* cr_;
+    //! The multisim record
+    const gmx_multisim_t* ms_;
     //! MDLogger for notifications during mdrun
     const MDLogger* logger_ = nullptr;
 
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy b/gromacs/src/applied_forces/colvars/tests/.clang-tidy
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/.clang-tidy
rename to gromacs/src/applied_forces/colvars/tests/.clang-tidy
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt b/gromacs/src/applied_forces/colvars/tests/CMakeLists.txt
similarity index 92%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt
rename to gromacs/src/applied_forces/colvars/tests/CMakeLists.txt
index c47edb16e..1d7198d79 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/CMakeLists.txt
+++ b/gromacs/src/applied_forces/colvars/tests/CMakeLists.txt
@@ -48,6 +48,11 @@ else()
         )
 endif()
 
+if(GMX_LIB_MPI)
+    # THis target does not link the library directly, must add the flag again
+    target_compile_definitions(colvars_applied_forces-test PRIVATE -DCOLVARS_MPI)
+endif()
+
 target_link_libraries(colvars_applied_forces-test PRIVATE applied_forces math topology mdlib
     mdtypes)
 
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp b/gromacs/src/applied_forces/colvars/tests/colvars.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars.cpp
rename to gromacs/src/applied_forces/colvars/tests/colvars.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat b/gromacs/src/applied_forces/colvars/tests/colvars_sample.dat
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample.dat
rename to gromacs/src/applied_forces/colvars/tests/colvars_sample.dat
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat b/gromacs/src/applied_forces/colvars/tests/colvars_sample_alanine.dat
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvars_sample_alanine.dat
rename to gromacs/src/applied_forces/colvars/tests/colvars_sample_alanine.dat
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp b/gromacs/src/applied_forces/colvars/tests/colvarsforceprovider.cpp
similarity index 97%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp
rename to gromacs/src/applied_forces/colvars/tests/colvarsforceprovider.cpp
index fbf3452d2..f51684413 100644
--- a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsforceprovider.cpp
+++ b/gromacs/src/applied_forces/colvars/tests/colvarsforceprovider.cpp
@@ -58,6 +58,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdrunutility/multisim.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/forceoutput.h"
@@ -202,6 +203,7 @@ TEST_F(ColvarsForceProviderTest, CanConstructOrNot)
                                                        seed_,
                                                        &atomSetManager_,
                                                        &cr_,
+                                                       nullptr,
                                                        simulationTimeStep_,
                                                        atomCoords_,
                                                        prefixOutput_,
@@ -227,6 +229,7 @@ TEST_F(ColvarsForceProviderTest, SimpleInputs)
                                        seed_,
                                        &atomSetManager_,
                                        &cr_,
+                                       nullptr,
                                        simulationTimeStep_,
                                        atomCoords_,
                                        prefixOutput_,
@@ -289,6 +292,7 @@ TEST_F(ColvarsForceProviderTest, WrongColvarsInput)
                                                         seed_,
                                                         &atomSetManager_,
                                                         &cr_,
+                                                        nullptr,
                                                         simulationTimeStep_,
                                                         atomCoords_,
                                                         prefixOutput_,
@@ -328,6 +332,7 @@ TEST_F(ColvarsForceProviderTest, CalculateForces4water)
                                        seed_,
                                        &atomSetManager_,
                                        &cr_,
+                                       nullptr,
                                        simulationTimeStep_,
                                        atomCoords_,
                                        prefixOutput_,
@@ -372,6 +377,7 @@ TEST_F(ColvarsForceProviderTest, CalculateForcesAlanine)
                                        seed_,
                                        &atomSetManager_,
                                        &cr_,
+                                       nullptr,
                                        simulationTimeStep_,
                                        atomCoords_,
                                        prefixOutput_,
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp b/gromacs/src/applied_forces/colvars/tests/colvarsoptions.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarsoptions.cpp
rename to gromacs/src/applied_forces/colvars/tests/colvarsoptions.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp b/gromacs/src/applied_forces/colvars/tests/colvarspreprocessor.cpp
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/colvarspreprocessor.cpp
rename to gromacs/src/applied_forces/colvars/tests/colvarspreprocessor.cpp
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx b/gromacs/src/applied_forces/colvars/tests/index.ndx
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/index.ndx
rename to gromacs/src/applied_forces/colvars/tests/index.ndx
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForces4water.xml
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsForceProviderTest_CalculateForcesAlanine.xml
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputDefaultValuesWhenActive.xml
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputNoDefaultValuesWhenInactive.xml
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsOptionsTest_OutputValuesWhenActive.xml
diff --git a/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml b/gromacs/src/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml
similarity index 100%
rename from gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml
rename to gromacs/src/applied_forces/colvars/tests/refdata/ColvarsPreProcessorTest_CheckValuesFourWaters.xml
diff --git a/gromacs/src/colvarproxy_gromacs_version.h b/gromacs/src/colvarproxy_gromacs_version.h
index 55ca42208..98fd8f2b4 100644
--- a/gromacs/src/colvarproxy_gromacs_version.h
+++ b/gromacs/src/colvarproxy_gromacs_version.h
@@ -1,43 +1,3 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright 2023- The GROMACS Authors
- * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
- * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
- *
- * 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
- * https://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 https://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out https://www.gromacs.org.
- */
-/*! \internal \file
- * \brief
- * Tracks the Colvars GROMACS interface version; see https://github.com/Colvars/colvars
-
- * \ingroup module_applied_forces
- */
-
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2023-12-05"
+#define COLVARPROXY_VERSION "2024-10-05"
 #endif
diff --git a/gromacs/tests/interface/010_MPI_multi-sim/run.sh b/gromacs/tests/interface/010_MPI_multi-sim/run.sh
index 680354eb1..261f1eb0f 100755
--- a/gromacs/tests/interface/010_MPI_multi-sim/run.sh
+++ b/gromacs/tests/interface/010_MPI_multi-sim/run.sh
@@ -5,17 +5,42 @@
 # It's best to have Gromacs compiled in double precision
 # Reference files have been generated with Gromacs version 2024-dev
 
+echo -n "Running $(basename $PWD)..."
+
+set -e
+
 # if script called from `run_tests.sh` in the parent folder, retrieve the correct command binary from the argument
-if [ "$1" ]
+if [ -x "$1" ]
 then
     BINARY=$1
 else
     BINARY="gmx_mpi_d"
 fi
 
-mpirun -np 16 -oversubscribe $BINARY mdrun -multidir a b c d -s test.tpr -deffnm test -replex 10 -reseed 376 2>&1 | tee test.out
+mpirun -np 16 -oversubscribe $BINARY mdrun -multidir a b c d -s test.tpr -deffnm test -replex 10 -reseed 376 >& test.out
+
+labels=(a b c d)
+for number in $(seq 1 ${#labels[@]}) ; do
+  index=$((${number} - 1))
+  label=${labels[${index}]}
+  replica_msg=$(grep -s "colvars: Enabling multiple replicas: this is replica number" ${label}/test.log)
+  if [ -z "${replica_msg}" ] ; then
+    echo "Error: missing replica initialization message." >& 2
+    exit 1
+  fi
+  replica_num=$(echo ${replica_msg} | cut -d' ' -f 9)
+  replicas_count=$(echo ${replica_msg} | cut -d' ' -f 11)
+  replicas_count=${replicas_count%.}
+  if [ ${replicas_count} != 4 ] || [ ${replica_num} != ${number} ] ; then
+    echo -e "Error: wrong initialization for replica number ${number}; got the following message:\n\n${replica_msg}\n" >& 2
+    exit 1
+  fi
+done
+
+# # TODO actually test these against the reference
+# # Copy result files to be tested in the main folder
+# cp -f a/test.colvars.traj a/test.colvars.state .
+# cp -f a/test.log ./test.out
 
-# Copy result files to be tested in the main folder
-cp a/test.colvars.traj a/test.colvars.state .
-cp a/test.log ./test.out
+echo " Success!"
 
diff --git a/gromacs/tests/interface/run_tests.sh b/gromacs/tests/interface/run_tests.sh
index 5988dae79..913ec3d2e 100755
--- a/gromacs/tests/interface/run_tests.sh
+++ b/gromacs/tests/interface/run_tests.sh
@@ -20,13 +20,13 @@ fi
 
 # Run tests that depend on an MPI build
 if source ${TOPDIR}/devel-tools/load-openmpi.sh ; then
-    if cd 010_MPI_multi-sim ; then
+    if pushd 010_MPI_multi-sim > /dev/null ; then
         ./run.sh $1
         if [ $? -ne 0 ]
         then
             ALL_SUCCESS=0
         fi
-        cd -
+        popd > /dev/null
     fi
 fi
 
diff --git a/gromacs/tests/library/Common/test.mdp b/gromacs/tests/library/Common/test.mdp
index 693f18d42..c3953c389 100644
--- a/gromacs/tests/library/Common/test.mdp
+++ b/gromacs/tests/library/Common/test.mdp
@@ -53,6 +53,5 @@ tcoupl                   = no
 gen_vel                  = no
 
 ; Colvars configuration
-colvars-active           = yes
+colvars-active           = Yes
 colvars-configfile       = test.in
-colvars-seed             = 12345
diff --git a/gromacs/tests/library/run_tests.sh b/gromacs/tests/library/run_tests.sh
index 86fb1243d..d08e90bb1 100755
--- a/gromacs/tests/library/run_tests.sh
+++ b/gromacs/tests/library/run_tests.sh
@@ -109,21 +109,12 @@ else
   MDMODULES_INTERFACE=no
 fi
 
-TORCH_LINKED=false
-# Need readlink because ldd can give wrong results when run on symlinks to binaries
-if { ldd $(readlink -f $(which $BINARY)) | grep -q libtorch[_a-zA-Z]*.so ; } then TORCH_LINKED=true ; fi
-
 for dir in ${DIRLIST} ; do
 
   if [ -f ${dir}/disabled ] ; then
     continue
   fi
 
-  if echo ${dir} | grep -q torchann && [ ${TORCH_LINKED} != "true" ] ; then 
-    echo "Binary is not libtorch-enabled; directory ${dir} skipped."
-    continue
-  fi
-
   echo -ne "Entering $(${TPUT_BLUE})${dir}$(${TPUT_CLEAR}) ..."
   cd $dir
 
diff --git a/lammps/COLVARS.cmake.diff b/lammps/COLVARS.cmake.diff
index 7b989d4bf..daea8d459 100644
--- a/lammps/COLVARS.cmake.diff
+++ b/lammps/COLVARS.cmake.diff
@@ -1,15 +1,14 @@
 diff --git a/cmake/Modules/Packages/COLVARS.cmake b/cmake/Modules/Packages/COLVARS.cmake
-index 745c1de026..b943a0345e 100644
+index b943a0345e..ebee306f43 100644
 --- a/cmake/Modules/Packages/COLVARS.cmake
 +++ b/cmake/Modules/Packages/COLVARS.cmake
-@@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
- target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
- target_link_libraries(lammps PRIVATE colvars)
+@@ -30,6 +30,11 @@ if(BUILD_OMP)
+   target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
+ endif()
  
-+if(BUILD_OMP)
-+  # Enable OpenMP for Colvars as well
-+  target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
-+  target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
++if(BUILD_MPI)
++  target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
++  target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
 +endif()
 +
  if(COLVARS_DEBUG)
diff --git a/lammps/src/COLVARS/colvarproxy_lammps.cpp b/lammps/src/COLVARS/colvarproxy_lammps.cpp
index 37fe4ab0a..c34e2e0fd 100644
--- a/lammps/src/COLVARS/colvarproxy_lammps.cpp
+++ b/lammps/src/COLVARS/colvarproxy_lammps.cpp
@@ -41,9 +41,6 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp)
   previous_step = -1;
   do_exit = false;
 
-  inter_me = 0;
-  inter_num = 1;
-
   engine_ready_ = false;
 }
 
@@ -91,17 +88,6 @@ void colvarproxy_lammps::set_random_seed(int seed)
 }
 
 
-void colvarproxy_lammps::set_replicas_communicator(MPI_Comm root2root)
-{
-  inter_comm = root2root;
-  // initialize multi-replica support, if available
-  if (replica_enabled() == COLVARS_OK) {
-    MPI_Comm_rank(inter_comm, &inter_me);
-    MPI_Comm_size(inter_comm, &inter_num);
-  }
-}
-
-
 // re-initialize data where needed
 int colvarproxy_lammps::setup()
 {
@@ -260,58 +246,6 @@ int colvarproxy_lammps::set_unit_system(std::string const &units_in, bool /*chec
 }
 
 
-// multi-replica support
-
-int colvarproxy_lammps::replica_enabled()
-{
-  return (inter_comm != MPI_COMM_NULL) ? COLVARS_OK : COLVARS_NOT_IMPLEMENTED;
-}
-
-
-int colvarproxy_lammps::replica_index()
-{
-  return inter_me;
-}
-
-
-int colvarproxy_lammps::num_replicas()
-{
-  return inter_num;
-}
-
-
-void colvarproxy_lammps::replica_comm_barrier()
-{
-  MPI_Barrier(inter_comm);
-}
-
-
-int colvarproxy_lammps::replica_comm_recv(char* msg_data,
-                                          int buf_len, int src_rep)
-{
-  MPI_Status status;
-  int retval;
-
-  retval = MPI_Recv(msg_data,buf_len,MPI_CHAR,src_rep,0,inter_comm,&status);
-  if (retval == MPI_SUCCESS) {
-    MPI_Get_count(&status, MPI_CHAR, &retval);
-  } else retval = 0;
-  return retval;
-}
-
-
-int colvarproxy_lammps::replica_comm_send(char* msg_data,
-                                          int msg_len, int dest_rep)
-{
-  int retval;
-  retval = MPI_Send(msg_data,msg_len,MPI_CHAR,dest_rep,0,inter_comm);
-  if (retval == MPI_SUCCESS) {
-    retval = msg_len;
-  } else retval = 0;
-  return retval;
-}
-
-
 
 int colvarproxy_lammps::check_atom_id(int atom_number)
 {
diff --git a/lammps/src/COLVARS/colvarproxy_lammps.h b/lammps/src/COLVARS/colvarproxy_lammps.h
index 80939a1c1..7ed469baa 100644
--- a/lammps/src/COLVARS/colvarproxy_lammps.h
+++ b/lammps/src/COLVARS/colvarproxy_lammps.h
@@ -41,9 +41,6 @@ class colvarproxy_lammps : public colvarproxy {
 
   std::vector<int> atoms_types;
 
-  MPI_Comm inter_comm;        // MPI comm with 1 root proc from each world
-  int inter_me, inter_num;    // rank for the inter replica comm
-
  public:
   friend class cvm::atom;
 
@@ -56,9 +53,6 @@ class colvarproxy_lammps : public colvarproxy {
   /// Set the internal seed used by \link rand_gaussian() \endlink
   void set_random_seed(int seed);
 
-  /// Set the multiple replicas communicator
-  void set_replicas_communicator(MPI_Comm root2root);
-
   int setup() override;
 
   // disable default and copy constructor
@@ -99,14 +93,6 @@ class colvarproxy_lammps : public colvarproxy {
   int check_atom_id(int atom_number) override;
 
   inline std::vector<int> *modify_atom_types() { return &atoms_types; }
-
-  int replica_enabled() override;
-  int replica_index() override;
-  int num_replicas() override;
-
-  void replica_comm_barrier() override;
-  int replica_comm_recv(char *msg_data, int buf_len, int src_rep) override;
-  int replica_comm_send(char *msg_data, int msg_len, int dest_rep) override;
 };
 
 #endif
diff --git a/lammps/src/COLVARS/colvarproxy_lammps_version.h b/lammps/src/COLVARS/colvarproxy_lammps_version.h
index 5901044b1..98fd8f2b4 100644
--- a/lammps/src/COLVARS/colvarproxy_lammps_version.h
+++ b/lammps/src/COLVARS/colvarproxy_lammps_version.h
@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2024-07-05"
+#define COLVARPROXY_VERSION "2024-10-05"
 #endif
diff --git a/lammps/src/COLVARS/fix_colvars.cpp b/lammps/src/COLVARS/fix_colvars.cpp
index d2da1416d..b1ee0cbac 100644
--- a/lammps/src/COLVARS/fix_colvars.cpp
+++ b/lammps/src/COLVARS/fix_colvars.cpp
@@ -286,7 +286,7 @@ void FixColvars::init()
     }
     MPI_Comm_split(universe->uworld, color, universe->iworld, &root2root);
     if (me == 0) {
-      proxy->set_replicas_communicator(root2root);
+      proxy->set_replicas_mpi_communicator(root2root);
     }
   }
 }
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 2cbc0a59e..57036261b 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -1605,7 +1605,7 @@ int colvarproxy_namd::smp_biases_script_loop()
 #endif  // #if CMK_SMP && USE_CKLOOP
 
 
-int colvarproxy_namd::replica_enabled() {
+int colvarproxy_namd::check_replicas_enabled() {
 #if CMK_HAS_PARTITION
   return COLVARS_OK;
 #else
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index dd7d88ffb..3aff50295 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -167,7 +167,7 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster {
 
 #endif // #if CMK_SMP && USE_CKLOOP
 
-  int replica_enabled() override;
+  int check_replicas_enabled() override;
   int replica_index() override;
   int num_replicas() override;
   void replica_comm_barrier() override;
diff --git a/namd/src/colvarproxy_namd_version.h b/namd/src/colvarproxy_namd_version.h
index 21077698c..98fd8f2b4 100644
--- a/namd/src/colvarproxy_namd_version.h
+++ b/namd/src/colvarproxy_namd_version.h
@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2023-12-05"
+#define COLVARPROXY_VERSION "2024-10-05"
 #endif
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
index 632765086..6744d6a8f 100644
--- a/src/colvarbias_abf.cpp
+++ b/src/colvarbias_abf.cpp
@@ -87,7 +87,7 @@ int colvarbias_abf::init(std::string const &conf)
   get_keyval(conf, "shared", shared_on, false);
   if (shared_on) {
     cvm::main()->cite_feature("Multiple-walker ABF implementation");
-    if ((proxy->replica_enabled() != COLVARS_OK) ||
+    if ((proxy->check_replicas_enabled() != COLVARS_OK) ||
         (proxy->num_replicas() <= 1)) {
       return cvm::error("Error: shared ABF requires more than one replica.",
                         COLVARS_INPUT_ERROR);
@@ -525,7 +525,7 @@ int colvarbias_abf::replica_share() {
 
   colvarproxy *proxy = cvm::main()->proxy;
 
-  if (proxy->replica_enabled() != COLVARS_OK) {
+  if (proxy->check_replicas_enabled() != COLVARS_OK) {
     cvm::error("Error: shared ABF: No replicas.\n");
     return COLVARS_ERROR;
   }
diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp
index 637bfa820..e95352fbe 100644
--- a/src/colvarbias_meta.cpp
+++ b/src/colvarbias_meta.cpp
@@ -209,7 +209,7 @@ int colvarbias_meta::init_replicas_params(std::string const &conf)
 
     get_keyval(conf, "replicaID", replica_id, replica_id);
     if (!replica_id.size()) {
-      if (proxy->replica_enabled() == COLVARS_OK) {
+      if (proxy->check_replicas_enabled() == COLVARS_OK) {
         // Obtain replicaID from the communicator
         replica_id = cvm::to_str(proxy->replica_index());
         cvm::log("Setting replicaID from communication layer: replicaID = "+
diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp
index 25b1efe20..5681660c0 100644
--- a/src/colvarmodule.cpp
+++ b/src/colvarmodule.cpp
@@ -129,6 +129,17 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
     }
   }
 
+  if (proxy->check_replicas_enabled() == COLVARS_NOT_IMPLEMENTED) {
+    cvm::log("  - Multiple replicas: not available\n");
+  } else {
+    if (proxy->check_replicas_enabled() == COLVARS_OK) {
+      cvm::log("  - Multiple replicas: enabled (replica number " +
+               to_str(proxy->replica_index() + 1) + " of " + to_str(proxy->num_replicas()) + ")\n");
+    } else {
+      cvm::log("  - Multiple replicas: available, but not (yet) enabled\n");
+    }
+  }
+
 #if defined(LEPTON)
   cvm::log("  - Lepton custom functions: available\n");
 #else
diff --git a/src/colvarproxy.h b/src/colvarproxy.h
index 91db6011e..6f3fd1b28 100644
--- a/src/colvarproxy.h
+++ b/src/colvarproxy.h
@@ -13,6 +13,7 @@
 #include "colvarmodule.h"
 #include "colvartypes.h"
 #include "colvarproxy_io.h"
+#include "colvarproxy_replicas.h"
 #include "colvarproxy_system.h"
 #include "colvarproxy_tcl.h"
 #include "colvarproxy_volmaps.h"
@@ -491,38 +492,6 @@ class colvarproxy_smp {
 };
 
 
-/// \brief Methods for multiple-replica communication
-class colvarproxy_replicas {
-
-public:
-
-  /// Constructor
-  colvarproxy_replicas();
-
-  /// Destructor
-  virtual ~colvarproxy_replicas();
-
-  /// \brief Indicate if multi-replica support is available and active
-  virtual int replica_enabled();
-
-  /// \brief Index of this replica
-  virtual int replica_index();
-
-  /// \brief Total number of replicas
-  virtual int num_replicas();
-
-  /// \brief Synchronize replica with others
-  virtual void replica_comm_barrier();
-
-  /// \brief Receive data from other replica
-  virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
-
-  /// \brief Send data to other replica
-  virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
-
-};
-
-
 /// Methods for scripting language interface (Tcl or Python)
 class colvarproxy_script {
 
diff --git a/src/colvarproxy_replicas.cpp b/src/colvarproxy_replicas.cpp
index 1f336d3e4..ec7ffdd8d 100644
--- a/src/colvarproxy_replicas.cpp
+++ b/src/colvarproxy_replicas.cpp
@@ -7,50 +7,103 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+
 #include "colvarmodule.h"
-#include "colvarproxy.h"
+#include "colvarproxy_replicas.h"
 
 
-colvarproxy_replicas::colvarproxy_replicas() {}
+colvarproxy_replicas::colvarproxy_replicas()
+{
+#ifdef COLVARS_MPI
+  replicas_mpi_comm = MPI_COMM_NULL;
+#endif
+}
 
 
 colvarproxy_replicas::~colvarproxy_replicas() {}
 
 
-int colvarproxy_replicas::replica_enabled()
+void colvarproxy_replicas::set_replicas_mpi_communicator(replicas_mpi_comm_t comm)
 {
+  replicas_mpi_comm = comm;
+#ifdef COLVARS_MPI
+  if (comm != MPI_COMM_NULL) {
+    MPI_Comm_rank(comm, &replicas_mpi_rank);
+    MPI_Comm_size(comm, &replicas_mpi_num);
+    cvm::log("Enabling multiple replicas: this is replica number " +
+             cvm::to_str(replica_index() + 1) + " of " + cvm::to_str(num_replicas()) + ".\n");
+  }
+#endif
+}
+
+
+int colvarproxy_replicas::check_replicas_enabled()
+{
+#ifdef COLVARS_MPI
+  if (replicas_mpi_comm != MPI_COMM_NULL) {
+    return num_replicas() > 1 ? COLVARS_OK : COLVARS_ERROR;
+  }
+  return COLVARS_ERROR;
+#else
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
 int colvarproxy_replicas::replica_index()
 {
-  return 0;
+  return replicas_mpi_rank;
 }
 
 
 int colvarproxy_replicas::num_replicas()
 {
-  return 1;
+  return replicas_mpi_num;
 }
 
 
-void colvarproxy_replicas::replica_comm_barrier() {}
+void colvarproxy_replicas::replica_comm_barrier()
+{
+#ifdef COLVARS_MPI
+  MPI_Barrier(replicas_mpi_comm);
+#endif
+}
 
 
-int colvarproxy_replicas::replica_comm_recv(char* /* msg_data */,
-                                            int /* buf_len */,
-                                            int /* src_rep */)
+int colvarproxy_replicas::replica_comm_recv(char *buffer, int buffer_length, int source_rank)
 {
+#ifdef COLVARS_MPI
+  MPI_Status status;
+  int retval = MPI_Recv(buffer, buffer_length, MPI_CHAR, source_rank, 0, replicas_mpi_comm, &status);
+  if (retval == MPI_SUCCESS) {
+    MPI_Get_count(&status, MPI_CHAR, &retval);
+  } else {
+    retval = 0;
+  }
+  return retval;
+#else
+  (void)buffer;
+  (void)buffer_length;
+  (void)source_rank;
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
 
 
-int colvarproxy_replicas::replica_comm_send(char* /* msg_data */,
-                                            int /* msg_len */,
-                                            int /* dest_rep */)
+int colvarproxy_replicas::replica_comm_send(char *buffer, int buffer_length, int destination_rank)
 {
+#ifdef COLVARS_MPI
+  int retval = MPI_Send(buffer, buffer_length, MPI_CHAR, destination_rank, 0, replicas_mpi_comm);
+  if (retval == MPI_SUCCESS) {
+    retval = buffer_length;
+  } else {
+    retval = 0;
+  }
+  return retval;
+#else
+  (void)buffer;
+  (void)buffer_length;
+  (void)destination_rank;
   return COLVARS_NOT_IMPLEMENTED;
+#endif
 }
-
-
diff --git a/src/colvarproxy_replicas.h b/src/colvarproxy_replicas.h
new file mode 100644
index 000000000..b58c80bf5
--- /dev/null
+++ b/src/colvarproxy_replicas.h
@@ -0,0 +1,66 @@
+// -*- c++ -*-
+
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/Colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+#ifndef COLVARPROXY_REPLICAS_H
+#define COLVARPROXY_REPLICAS_H
+
+
+#ifdef COLVARS_MPI
+#include <mpi.h>
+typedef MPI_Comm replicas_mpi_comm_t;
+#else
+typedef void * replicas_mpi_comm_t;
+#endif
+
+
+/// \brief Methods for multiple-replica communication
+class colvarproxy_replicas {
+
+public:
+
+  /// Constructor
+  colvarproxy_replicas();
+
+  /// Destructor
+  virtual ~colvarproxy_replicas();
+
+  /// Set the multiple replicas communicator
+  virtual void set_replicas_mpi_communicator(replicas_mpi_comm_t comm);
+
+  /// Indicate if multi-replica support is available and active
+  virtual int check_replicas_enabled();
+
+  /// Index of this replica
+  virtual int replica_index();
+
+  /// Total number of replicas
+  virtual int num_replicas();
+
+  /// Synchronize replica with others
+  virtual void replica_comm_barrier();
+
+  /// Receive data from other replica
+  virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
+
+  /// Send data to other replica
+  virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
+
+protected:
+
+  /// MPI communicator containint 1 root proc from each world
+  replicas_mpi_comm_t replicas_mpi_comm;
+
+  /// Index (rank) of this replica in the MPI implementation
+  int replicas_mpi_rank = 0;
+
+  /// Number of replicas in the MPI implementation
+  int replicas_mpi_num = 1;
+};
+
+#endif
diff --git a/src/colvars_version.h b/src/colvars_version.h
index 02d8cd4f9..5db618e80 100644
--- a/src/colvars_version.h
+++ b/src/colvars_version.h
@@ -1,3 +1,3 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2024-09-17"
+#define COLVARS_VERSION "2024-10-05"
 #endif
diff --git a/update-colvars-code.sh b/update-colvars-code.sh
index 319eb0921..447c3aa1b 100755
--- a/update-colvars-code.sh
+++ b/update-colvars-code.sh
@@ -109,9 +109,9 @@ else
 fi
 
 if [ ${code} == "GROMACS" ] ; then
-  if [ -f ${target}/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp ] ; then
-    # Code after https://gitlab.com/gromacs/gromacs/-/merge_requests/3566
-    code=GROMACS-DEV
+  if [ ! -f ${target}/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp ] ; then
+    echo "ERROR: Versions of GROMACS prior to 2024 are no longer supported."
+    exit 1
   fi
 fi
 
@@ -184,46 +184,15 @@ then
     exit 3
   fi
 
-  GMX_MAJOR_VERSION=`get_gromacs_major_version_cmake ${GMX_VERSION_INFO}`
-  GMX_MINOR_VERSION=`get_gromacs_minor_version_cmake ${GMX_VERSION_INFO}`
-
-  GMX_VERSION=${GMX_MAJOR_VERSION}.${GMX_MINOR_VERSION}
-
-  # Since 2022, version info is in CMakeLists.txt
-  if [ ${GMX_MAJOR_VERSION} = "\${Gromacs_VERSION_MAJOR}" ] ; then
-    CMAKE_LISTS=${target}/CMakeLists.txt
-    if [ ! -f ${CMAKE_LISTS} ] ; then
-      echo "ERROR: Cannot find file ${CMAKE_LISTS}."
-      exit 3
-    fi
-    GMX_VERSION=$(cat ${CMAKE_LISTS} | grep '^project(' | \
-    sed -e 's/project(Gromacs VERSION //' -e 's/)//')
+  CMAKE_LISTS=${target}/CMakeLists.txt
+  if [ ! -f ${CMAKE_LISTS} ] ; then
+    echo "ERROR: Cannot find file ${CMAKE_LISTS}."
+    exit 3
   fi
+  GMX_VERSION=$(cat ${CMAKE_LISTS} | grep '^project(' | sed -e 's/project(Gromacs VERSION //' -e 's/)//')
 
   echo "Detected GROMACS version ${GMX_VERSION}."
 
-  case ${GMX_VERSION} in
-    2023*)
-      GMX_VERSION='2023.x'
-      ;;
-    *)
-    if [ $force_update = 0 ] ; then
-      echo " ******************************************************************************"
-      echo "  ERROR: GROMACS version ${GMX_VERSION} is unsupported."
-      echo "  You may override with -f, but be mindful of compilation or runtime problems."
-      echo "  Alternatively, you may also download legacy code versions at https://github.com/Colvars/gromacs"
-      echo " ******************************************************************************"
-      exit 3
-    else
-      echo " ******************************************************************************"
-      echo "  WARNING: Unsupported GROMACS ${GMX_VERSION} version will be patched."
-      echo "           Using GROMACS 2023.x files for patching."
-      echo " ******************************************************************************"
-      GMX_VERSION='2023.x'
-    fi
-    ;;
-  esac
-
   if [ -z "${GITHUB_ACTION}" ] ; then
     # Only set version outside CI to avoid invalidating the compiler cache
     if grep -q 'set(GMX_VERSION_STRING_OF_FORK ""' ${GMX_VERSION_INFO} ; then
@@ -232,6 +201,7 @@ then
   fi
 
 fi
+
 echo -n "Updating ..."
 
 
@@ -312,11 +282,6 @@ then
     condcopy "${src}" "${target}/lib/colvars/${tgt}"
   done
 
-  # Update cmake file 
-  src=${source}/lammps/COLVARS.cmake
-  tgt=$(basename ${src})
-  condcopy "${source}/lammps/COLVARS.cmake" "${target}/cmake/Modules/Packages/${tgt}"
-
   for src in \
     ${source}/lammps/src/COLVARS/colvarproxy_lammps{.cpp,.h,_version.h} \
     ${source}/lammps/src/COLVARS/fix_colvars.{cpp,h} \
@@ -393,10 +358,6 @@ then
     fi
   fi
 
-  # For torchann
-  patch -F 12 -p1 -N -d ${target} < namd/config.patch
-  sed -i '/^COLVARSCXXFLAGS =*/s/$/ $(EXTRACOLVARSFLAGS)/' ${target}/Makefile
-
   # Copy library files to the "colvars" folder
   for src in ${source}/src/*.h ${source}/src/*.cpp
   do \
@@ -528,107 +489,9 @@ then
   echo ' done.'
 fi
 
-# Update GROMACS tree (legacy versions)
-if [ ${code} = "GROMACS" ]
-then
-
-  if [ "x${UPDATE_LEPTON}" == "xyes" ] ; then
-    echo -n "(note: adding/updating Lepton)"
-    copy_lepton ${target}/src/external/ || exit 1
-  fi
-
-  target_folder=${target}/src/external/colvars
-  patch_opts="-p1 --forward -s"
-
-  echo ""
-  if [ -d ${target_folder} ]
-  then
-    echo "${target} source tree seems to have already been patched."
-    echo "Updating to the current Colvars sources."
-  else
-    mkdir ${target_folder}
-  fi
-
-  if [ ${GMX_VERSION} == '2020.x' ] || [ ${GMX_VERSION} == '2021.x' ] ; then
-    # Copy library files and proxy files to the "src/external/colvars" folder
-    for src in ${source}/src/*.h ${source}/src/*.cpp ${source}/gromacs/src/*.h ${source}/gromacs/gromacs-${GMX_VERSION}/*{cpp,h}
-    do \
-      tgt=$(basename ${src})
-      condcopy "${src}" "${target_folder}/${tgt}"
-    done
-  else
-    # Starting from GROMACS 2022, the Colvars library is under `external` and proxy files are in `src/gromacs/applied_forces/colvarproxy`
-    # Library files
-    for src in ${source}/src/*.h ${source}/src/*.cpp
-    do \
-      tgt=$(basename ${src})
-      condcopy "${src}" "${target_folder}/${tgt}"
-    done
-    # Proxy files
-    target_folder=${target}/src/gromacs/applied_forces/colvars
-    if [ -d ${target_folder} ]
-    then
-      echo "${target} source tree seems to have already been patched."
-      echo "Updating to the current Colvars sources."
-    else
-      mkdir ${target_folder}
-    fi
-    for src in ${source}/gromacs/src/*.h ${source}/gromacs/gromacs-${GMX_VERSION}/*{cpp,h,txt}
-    do \
-      tgt=$(basename ${src})
-      condcopy "${src}" "${target_folder}/${tgt}"
-    done
-
-  fi
-  echo ""
-
-  # Copy CMake files
-  condcopy "${source}/gromacs/cmake/gmxManageColvars.cmake" \
-           "${target}/cmake/gmxManageColvars.cmake"
-  if [ "x${UPDATE_LEPTON}" == "xyes" ] ; then
-    echo -n "(note: adding/updating Lepton)"
-    condcopy "${source}/gromacs/cmake/gmxManageLepton.cmake" \
-             "${target}/cmake/gmxManageLepton.cmake"
-  fi
-
-  # Apply patch for Gromacs files
-  patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-${GMX_VERSION}.patch
-  ret_val=$?
-  if [ $ret_val -ne 0 ]
-  then
-    echo " ************************************************************************* "
-    echo " Patch fails. It seems the Gromacs source files have been already patched. "
-    echo " ************************************************************************* "
-  else
-    echo ' done.'
-    echo ""
-    echo "  *******************************************"
-    echo "    Please create your build with cmake now."
-    echo "  *******************************************"
-  fi
-
-  if [ ${GMX_VERSION} == '2021.x' ] ; then
-    if [ -f "${target}/.github/workflows/build_cmake.yml" ] ; then
-      # Ad-hoc fix for CI build until 2021.6 is released
-      sed -i -e 's/windows-latest/windows-2019/' "${target}/.github/workflows/build_cmake.yml"
-    fi
-  fi
-
-  # Update the proxy version if needed
-  shared_gmx_proxy_version=$(grep '^#define' "${source}/gromacs/src/colvarproxy_gromacs_version.h" | cut -d' ' -f 3)
-
-  patch_gmx_proxy_version=$(grep '^#define' "${target_folder}/colvarproxy_gromacs_version.h" | cut -d' ' -f 3)
-
-  if [ ${shared_gmx_proxy_version} \> ${patch_gmx_proxy_version} ] ; then
-    condcopy ${source}/gromacs/src/colvarproxy_gromacs_version.h \
-      "${target}/src/gromacs/colvars/colvarproxy_gromacs_version.h"
-  fi
-
-  exit 0
-fi
 
 # Update GROMACS tree (MDModules interface-ready version)
-if [ ${code} = "GROMACS-DEV" ]
+if [ ${code} = "GROMACS" ]
 then
 
   target_folder=${target}/src/external/colvars
@@ -645,11 +508,11 @@ then
   echo ""
 
   # Patch CMake build recipes when applicable
-  if [ -s ${source}/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules/gmxManageColvars.cmake.diff || true
+  if [ -s ${source}/gromacs/gmxManageColvars.cmake.diff ] ; then
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/gmxManageColvars.cmake.diff || true
   fi
-  if [ -s ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.diff ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.diff || true
+  if [ -s ${source}/gromacs/CMakeLists.txt.diff ] ; then
+    patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.diff || true
   fi
   if [ -s ${source}/gromacs/CMakeLists.txt.diff ] ; then
     patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.diff || true
@@ -658,15 +521,15 @@ then
   if [ "x${UPDATE_LEPTON}" == "xyes" ] ; then
     echo -n "(note: adding/updating Lepton)"
     copy_lepton ${target}/src/external/ || exit 1
-    if [ -s ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.Lepton.diff ] ; then
-      patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules/CMakeLists.txt.Lepton.diff || true
+    if [ -s ${source}/gromacs/CMakeLists.txt.Lepton.diff ] ; then
+      patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.Lepton.diff || true
     fi
     condcopy ${source}/gromacs/cmake/gmxManageLepton.cmake "${target}/cmake/gmxManageLepton.cmake"
   fi
 
   echo
 
-  # Copy MDModules files to the "src/gromacs/applied_forces/colvars" folder
+  # Copy MDModules files to the "src/gromacs/src/applied_forces/colvars" folder
   target_folder=${target}/src/gromacs/applied_forces/colvars
   if [ -d ${target_folder} ]
   then
@@ -677,15 +540,15 @@ then
     mkdir -p ${target_folder}/tests/refdata
   fi
   condcopy gromacs/src/colvarproxy_gromacs_version.h "${target_folder}/colvarproxy_gromacs_version.h"
-  for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/*.* ; do
+  for src in ${source}/gromacs/src/applied_forces/colvars/*.* ; do
     tgt=$(basename ${src})
     condcopy "${src}" "${target_folder}/${tgt}"
   done
-  for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/*.* ; do
+  for src in ${source}/gromacs/src/applied_forces/colvars/tests/*.* ; do
     tgt=$(basename ${src})
     condcopy "${src}" "${target_folder}/tests/${tgt}"
   done
-  for src in ${source}/gromacs/gromacs-mdmodules/applied_forces/colvars/tests/refdata/*.* ; do
+  for src in ${source}/gromacs/src/applied_forces/colvars/tests/refdata/*.* ; do
     tgt=$(basename ${src})
     condcopy "${src}" "${target_folder}/tests/refdata/${tgt}"
   done
diff --git a/vmd/src/colvarproxy_vmd_version.h b/vmd/src/colvarproxy_vmd_version.h
index 21077698c..98fd8f2b4 100644
--- a/vmd/src/colvarproxy_vmd_version.h
+++ b/vmd/src/colvarproxy_vmd_version.h
@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2023-12-05"
+#define COLVARPROXY_VERSION "2024-10-05"
 #endif
diff --git a/vmd/src/colvars_files.pl b/vmd/src/colvars_files.pl
index 10a6dab12..4482724da 100644
--- a/vmd/src/colvars_files.pl
+++ b/vmd/src/colvars_files.pl
@@ -43,10 +43,10 @@
                     'colvarproxy.C',
                     'colvarproxy_io.C',
                     'colvarproxy_replicas.C',
-                    'colvarproxy_volmaps.C',
                     'colvarproxy_system.C',
                     'colvarproxy_tcl.C',
                     'colvarproxy_vmd.C',
+                    'colvarproxy_volmaps.C',
                     'colvarscript.C',
                     'colvarscript_commands.C',
                     'colvarscript_commands_bias.C',
@@ -81,6 +81,7 @@
                     'colvarparse.h',
                     'colvarproxy.h',
                     'colvarproxy_io.h',
+                    'colvarproxy_replicas.h',
                     'colvarproxy_system.h',
                     'colvarproxy_tcl.h',
                     'colvarproxy_vmd.h',