then gromacs has been installed…But when I run a simulation with PLUMED:
gmx mdrun -ntmpi 1 -v -s pmf.tpr -plumed dat
I meet a error:
Program: gmx mdrun, version 2025.0
Source file: src/gromacs/applied_forces/plumed/plumedMDModule_stub.cpp (line 81)
Function: gmx::{anonymous}::PlumedMDModule::subscribeToSimulationSetupNotifications(gmx::MDModulesNotifiers*)::<lambda(const gmx::PlumedInputFilename&)>
Error in user input:
GROMACS is not compiled with the PLUMED interface, if you want to use -plumed
option, please reconfigure GROMACS with -DGMX_USE_PLUMED=ON.
For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
Can someone help me to use GROMACS with PLUMED?
Thanks a lot!
Hi,
It’s likely that something went wrong during configuration. Could you share your cmake output? Also, remember that to run a simulation with PLUMED, you have to first run e.g. export PLUMED_KERNEL=$plumed_prefix/lib/libPlumedKernel.so so that GROMACS knows where to find the library.
Also, you should not set -DGMX_TORCH=TORCH (in fact, you shouldn’t set it at all). If you want to configure GROMACS with support for neural network potentials, you have to tell it about your Libtorch installation, see the installation guide.
-- The C compiler identification is GNU 11.4.1
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Reason given by package: LAPACK could not be found because dependency BLAS could not be found.
-- Using GROMACS built-in LAPACK.
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-- Configuring done (12.0s)
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-- Build files have been written to: /opt/package/gromacs/gromacs-2025.0/build
When I run a simulation with PLUMED, the environment variable is set:
Hmm, this looks OK to me. Since you set GMX_USE_PLUMED=ON, cmake should issue a fatal error when it can’t create the interface. Can you make sure that you’re sourcing the correct GROMACS build when you try and run the simulation with PLUMED? Otherwise, this could be a bug.
Just to update: This should get fixed in the next patch release 2025.1, but in the meantime, as a simple workaround it seems to be enough to just run CMake twice.