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Add a patch for GROMACS 2026
There is no patch for GROMACS 2026, so `plumed patch -e` offers nothing newer than gromacs-2025.0 and there is no supported way to build a PLUMED-enabled GROMACS 2026. Applying the 2025.0 patch to 2026.4 does not work. GROMACS replaced the t_commrec plumbing with the MpiComm abstraction in db61f87e0a ("Use MpiComm in t_commrec"), so PlumedOptions now carries `const MpiComm* mpiComm_` instead of `const t_commrec* cr_`: $ plumed patch -p -e gromacs-2025.0 # on a 2026.4 tree patching file ./src/gromacs/applied_forces/plumed/plumedforceprovider.cpp Hunk plumed#3 FAILED at 113. 1 out of 4 hunks FAILED -- saving rejects to ...plumedforceprovider.cpp.rej patching file ./src/gromacs/CMakeLists.txt Reversed (or previously applied) patch detected! Skipping patch. 2 out of 2 hunks ignored -- saving rejects to ./src/gromacs/CMakeLists.txt.rej and six further files apply only with fuzz 5. The failing hunk is the one that hands PLUMED the multi-replica communicators, which is the most damaging thing to lose silently: `GREX setMPIIntercomm` is what populates PlumedMain::multi_sim_comm (GREX.cpp), so without it every multi-replica action degrades to a single replica without any error. The new patch is the 2025.0 one carried onto the 2026 API: * the GREX/multisim block uses MpiComm::isMainRank() and MpiComm::comm() * src/gromacs/CMakeLists.txt is dropped entirely -- GROMACS 2026 already calls gmx_manage_plumed() early, which is why those hunks reported as already applied * setNumOMPthreads is carried over from plumed#1435 * the replex_ plumbing, the PLUMED_LOG_FILE override and forcing GMX_USE_PLUMED=ON are unchanged in substance It also fixes one bug in GROMACS's own code. The same MpiComm commit rewrote - plumed_->cmd("setMPIComm", &options.cr_->mpi_comm_mygroup); + plumed_->cmd("setMPIComm", options.mpiComm_->comm()); dropping the address-of. MpiComm::comm() returns MPI_Comm by value, but PLUMED reads that argument as `*(const MPI_Comm*)` (Communicator::Set_comm), so where MPI_Comm is a pointer type this compiles and silently passes the wrong handle. The patch passes the address of a named local instead. This is worth reporting to GROMACS separately; until it is fixed there, any domain-decomposed PLUMED run on 2026 is affected. Verified on GROMACS 2026.4 with clang 20.1.1, OpenMPI 5.0.7 and libc++: * `plumed patch -p -e gromacs-2026.0` applies with no fuzz and no rejects, and `plumed patch -r` restores the tree byte-for-byte * the patched GROMACS builds clean (GMX_MPI=ON, GMX_THREAD_MPI=OFF, GMX_OPENMP=ON); the four changed translation units compile with no errors and no warnings * a two-replica `mdrun -multidir` run expands `@replicas:` to a different value per replica, which is only possible when multi_sim_comm has been set up Scope for 2027: the plumed module sources on GROMACS main are currently identical to release-2026, and the runner.cpp and mdmodulesnotifiers.h edits apply there unchanged; only the stored .preplumed snapshots would need regenerating once 2027 branches.
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‎patches/gromacs-2026.0.config‎

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function plumed_preliminary_test(){
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# check if the README contains the word GROMACS and if gromacs has been already configured
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grep -q GROMACS README 1>/dev/null 2>/dev/null
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}
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function plumed_patch_info(){
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cat << EOF
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A basic PLUMED interface is already present in GROMACS
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This patch previes extra features to be implemented in the official PLUMED integration in the next GROMACS version
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Patching must be done in the gromacs root directory _before_ the cmake command is invoked.
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The GROMACS integration has some improvements with the compatibility wiht the multi-threading implementation
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but it is still preferable to configure gromacs as
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cmake -DGMX_THREAD_MPI=OFF and add -DGMX_MPI=ON if you want to use MPI.
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To enable PLUMED in a gromacs simulation one should use
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mdrun with an extra -plumed flag. The flag can be used to
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specify the name of the PLUMED input file, e.g.:
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gmx mdrun -plumed plumed.dat
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For more information on gromacs you should visit http://www.gromacs.org
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EOF
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}
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plumed_before_patch(){
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plumed_patch_info
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}
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PLUMED_PATCH_NO_INCLUDE=true
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#this will be added later
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#PLUMED_PATCH_EXTRA_FILES="src/external/plumed/PlumedInclude.h src/external/plumed/PlumedKernel.cpp src/gromacs/applied_forces/plumed/PlumedOutside.cpp src/gromacs/applied_forces/plumed/PlumedOutside.h"

‎patches/gromacs-2026.0.diff/cmake/gmxManagePlumed.cmake‎

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#
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# This file is part of the GROMACS molecular simulation package.
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#
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# Copyright 2024- The GROMACS Authors
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# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
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# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
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#
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# GROMACS is free software; you can redistribute it and/or
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# modify it under the terms of the GNU Lesser General Public License
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# as published by the Free Software Foundation; either version 2.1
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# of the License, or (at your option) any later version.
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#
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# GROMACS is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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# Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with GROMACS; if not, see
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# https://www.gnu.org/licenses, or write to the Free Software Foundation,
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# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#
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# If you want to redistribute modifications to GROMACS, please
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# consider that scientific software is very special. Version
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# control is crucial - bugs must be traceable. We will be happy to
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# consider code for inclusion in the official distribution, but
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# derived work must not be called official GROMACS. Details are found
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# in the README & COPYING files - if they are missing, get the
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# official version at https://www.gromacs.org.
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#
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# To help us fund GROMACS development, we humbly ask that you cite
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# the research papers on the package. Check out https://www.gromacs.org.
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# Builds the interface to plumed and add the linkage to libPlumed
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gmx_option_multichoice(GMX_USE_PLUMED
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"Build the PLUMED wrapper with GROMACS"
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ON
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ON)
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mark_as_advanced(GMX_USE_PLUMED)
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function(gmx_manage_plumed)
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# Create a link target, leave it empty if the plumed option is not active
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add_library(plumedgmx INTERFACE)
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set (GMX_PLUMED_ACTIVE OFF PARENT_SCOPE)
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if(WIN32)
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if(GMX_USE_PLUMED STREQUAL "ON")
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message(FATAL_ERROR "PLUMED is not supported on Windows. Reconfigure with -DGMX_USE_PLUMED=OFF.")
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endif()
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elseif(NOT GMX_USE_PLUMED STREQUAL "OFF")
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include(CMakePushCheckState)
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cmake_push_check_state(RESET)
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set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_DL_LIBS})
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include(CheckFunctionExists)
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check_function_exists(dlopen HAVE_DLOPEN)
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cmake_pop_check_state()
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if(HAVE_DLOPEN)
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# Plumed.h compiled in c++ mode creates a fully inlined interface
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# So we just need to activate the directory in applied_forces
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set(PLUMED_DIR "${CMAKE_SOURCE_DIR}/src/external/plumed")
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target_link_libraries( plumedgmx INTERFACE ${CMAKE_DL_LIBS} )
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# The plumedgmx already exists, now we set it up:
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target_include_directories(plumedgmx SYSTEM INTERFACE $<BUILD_INTERFACE:${PLUMED_DIR}>)
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set (GMX_PLUMED_ACTIVE ON PARENT_SCOPE)
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else()
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if(GMX_USE_PLUMED STREQUAL "ON")
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message(FATAL_ERROR "PLUMED needs dlopen or anything equivalent. Reconfigure with -DGMX_USE_PLUMED=OFF.")
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else() # "AUTO"
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message(STATUS "PLUMED needs dlopen or anything equivalent. Disabling support.")
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endif()
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endif()
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endif()
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endfunction()

‎patches/gromacs-2026.0.diff/cmake/gmxManagePlumed.cmake.preplumed‎

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#
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# This file is part of the GROMACS molecular simulation package.
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#
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# Copyright 2024- The GROMACS Authors
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# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
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# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
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#
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# GROMACS is free software; you can redistribute it and/or
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# modify it under the terms of the GNU Lesser General Public License
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# as published by the Free Software Foundation; either version 2.1
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# of the License, or (at your option) any later version.
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#
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# GROMACS is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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# Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with GROMACS; if not, see
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# https://www.gnu.org/licenses, or write to the Free Software Foundation,
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# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#
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# If you want to redistribute modifications to GROMACS, please
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# consider that scientific software is very special. Version
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# control is crucial - bugs must be traceable. We will be happy to
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# consider code for inclusion in the official distribution, but
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# derived work must not be called official GROMACS. Details are found
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# in the README & COPYING files - if they are missing, get the
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# official version at https://www.gromacs.org.
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#
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# To help us fund GROMACS development, we humbly ask that you cite
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# the research papers on the package. Check out https://www.gromacs.org.
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# Builds the interface to plumed and add the linkage to libPlumed
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gmx_option_multichoice(GMX_USE_PLUMED
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"Build the PLUMED wrapper with GROMACS"
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AUTO
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AUTO ON OFF)
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mark_as_advanced(GMX_USE_PLUMED)
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function(gmx_manage_plumed)
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# Create a link target, leave it empty if the plumed option is not active
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add_library(plumedgmx INTERFACE)
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set (GMX_PLUMED_ACTIVE OFF PARENT_SCOPE)
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if(WIN32)
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if(GMX_USE_PLUMED STREQUAL "ON")
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message(FATAL_ERROR "PLUMED is not supported on Windows. Reconfigure with -DGMX_USE_PLUMED=OFF.")
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endif()
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elseif(NOT GMX_USE_PLUMED STREQUAL "OFF")
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include(CMakePushCheckState)
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cmake_push_check_state(RESET)
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set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_DL_LIBS})
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include(CheckFunctionExists)
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check_function_exists(dlopen HAVE_DLOPEN)
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cmake_pop_check_state()
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if(HAVE_DLOPEN)
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# Plumed.h compiled in c++ mode creates a fully inlined interface
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# So we just need to activate the directory in applied_forces
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set(PLUMED_DIR "${CMAKE_SOURCE_DIR}/src/external/plumed")
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target_link_libraries( plumedgmx INTERFACE ${CMAKE_DL_LIBS} )
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# The plumedgmx already exists, now we set it up:
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target_include_directories(plumedgmx SYSTEM INTERFACE $<BUILD_INTERFACE:${PLUMED_DIR}>)
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set (GMX_PLUMED_ACTIVE ON PARENT_SCOPE)
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else()
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if(GMX_USE_PLUMED STREQUAL "ON")
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message(FATAL_ERROR "PLUMED needs dlopen or anything equivalent. Reconfigure with -DGMX_USE_PLUMED=OFF.")
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else() # "AUTO"
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message(STATUS "PLUMED needs dlopen or anything equivalent. Disabling support.")
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endif()
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endif()
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endif()
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endfunction()

‎patches/gromacs-2026.0.diff/src/gromacs/applied_forces/plumed/plumedMDModule.cpp‎

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/*
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* This file is part of the GROMACS molecular simulation package.
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*
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* Copyright 2024- The GROMACS Authors
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* and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
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* Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
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*
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* GROMACS is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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*
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* GROMACS is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with GROMACS; if not, see
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* https://www.gnu.org/licenses, or write to the Free Software Foundation,
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* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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*
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* If you want to redistribute modifications to GROMACS, please
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* consider that scientific software is very special. Version
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* control is crucial - bugs must be traceable. We will be happy to
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* consider code for inclusion in the official distribution, but
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* derived work must not be called official GROMACS. Details are found
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* in the README & COPYING files - if they are missing, get the
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* official version at https://www.gromacs.org.
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*
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* To help us fund GROMACS development, we humbly ask that you cite
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* the research papers on the package. Check out https://www.gromacs.org.
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*/
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/*! \internal \file
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* \brief
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* Implements Plumed MDModule class
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*
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* \author Daniele Rapetti <drapetti@sissa.it>
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* \ingroup module_applied_forces
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*/
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#include "gmxpre.h"
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#include "plumedMDModule.h"
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#include <memory>
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#include <string>
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#include "gromacs/fileio/checkpoint.h"
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#include "gromacs/mdrunutility/mdmodulesnotifiers.h"
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#include "gromacs/mdtypes/imdmodule.h"
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#include "gromacs/utility/keyvaluetreebuilder.h"
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#include "plumedOptions.h"
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#include "plumedforceprovider.h"
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namespace gmx
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{
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namespace
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{
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/*! \internal
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* \brief Plumed module
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*
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* Class that implements the plumed MDModule
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*/
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class PlumedMDModule final : public IMDModule
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{
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public:
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//! \brief Construct the plumed module.
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explicit PlumedMDModule() = default;
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// Now callbacks for several kinds of MdModuleNotification are created
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// and subscribed, and will be dispatched correctly at run time
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// based on the type of the parameter required by the lambda.
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/*! \brief Requests to be notified during pre-processing.
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*
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* Plumed does not act during the preprocessing phase of a simulation, so the input are ignored
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*/
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void subscribeToPreProcessingNotifications(MDModulesNotifiers* /*notifier*/) override {}
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/*! \brief Subscribe to MDModules notifications for information needed just before the simulation.
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*/
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void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifier) override
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{
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// TODO: add a check for threadmpi (see #5104, https://gitlab.com/gromacs/gromacs/-/merge_requests/4367#note_2102475958, the manual and the force provider for the details)
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// Access the plumed filename this is used to activate the plumed module
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notifier->simulationSetupNotifier_.subscribe(
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[this](const PlumedInputFilename& plumedFilename)
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{
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this->options_.setPlumedFile(plumedFilename.plumedFilename_);
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this->options_.setReplex(plumedFilename.replex_);
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});
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// Retrieve the multi-simulation object, needed to set up PLUMED's
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// multi-replica communicator
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notifier->simulationSetupNotifier_.subscribe([this](const gmx_multisim_t* ms)
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{ this->options_.setMultisim(ms); });
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// Access the temperature if it is constant during the simulation
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notifier->simulationSetupNotifier_.subscribe(
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[this](const EnsembleTemperature& ensembleT)
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{ this->options_.setEnsembleTemperature(ensembleT); });
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// Access of the topology
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notifier->simulationSetupNotifier_.subscribe([this](const gmx_mtop_t& mtop)
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{ this->options_.setTopology(mtop); });
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// Retrieve the Communication Record during simulations setup
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notifier->simulationSetupNotifier_.subscribe([this](const MpiComm& mpiComm)
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{ this->options_.setComm(mpiComm); });
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// setting the simulation time step
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notifier->simulationSetupNotifier_.subscribe(
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[this](const SimulationTimeStep& simulationTimeStep)
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{ this->options_.setSimulationTimeStep(simulationTimeStep.delta_t); });
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// Retrieve the starting behavior
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notifier->simulationSetupNotifier_.subscribe(
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[this](const StartingBehavior& startingBehavior)
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{ this->options_.setStartingBehavior(startingBehavior); });
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// writing checkpoint data
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notifier->checkpointingNotifier_.subscribe(
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[this](MDModulesWriteCheckpointData /*checkpointData*/)
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{
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if (options_.active())
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{
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plumedForceProvider_->writeCheckpointData();
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}
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});
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}
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/*! \brief Subscribe to MDModules notifications for information needed during the simulation.
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*/
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void subscribeToSimulationRunNotifications(MDModulesNotifiers* notifier) override
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{
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if (!options_.active())
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{
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return;
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}
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// Retrieve the global atom indices
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notifier->simulationRunNotifier_.subscribe(
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[this](const MDModulesAtomsRedistributedSignal& atomsRedistributedSignal) {
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plumedForceProvider_->setGlobalAtomIndices(atomsRedistributedSignal.globalAtomIndices_);
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});
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}
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//! From IMDModule
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IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
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//! From IMDModule
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IMDOutputProvider* outputProvider() override
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{ // Plumed provide its own output
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return nullptr;
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}
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//! From IMDModule - Adds this module to the force providers if active
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void initForceProviders(ForceProviders* forceProviders) override
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{
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if (options_.active())
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{
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plumedForceProvider_ = std::make_unique<PlumedForceProvider>(options_.options());
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forceProviders->addForceProvider(plumedForceProvider_.get(),
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std::string(PlumedModuleInfo::sc_name));
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}
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}
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private:
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//! Parameters that become available at simulation setup time.
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PlumedOptionProvider options_{};
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//! Object that evaluates the forces
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std::unique_ptr<PlumedForceProvider> plumedForceProvider_{};
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};
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} // namespace
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std::unique_ptr<IMDModule> PlumedModuleInfo::create()
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{
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return std::make_unique<PlumedMDModule>();
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}
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std::string plumedDescription()
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{
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return "enabled";
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}
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} // namespace gmx

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