PLUMED can be incorporated into gromacs using the standard patching procedure. Patching must be done in the gromacs root directory before the cmake command is invoked.

PLUMED is not compatible with the internal multi-threading implementation of GROMACS so you need to configure gromacs as

cmake -DGMX_THREAD_MPI=OFF and add -DGMX_MPI=ON if you want to use MPI.

On clusters you may want to patch gromacs using the static version of plumed, in this case building gromacs can result in multiple errors. One possible solution is to configure gromacs with these additional options:

cmake -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON

To enable PLUMED in a gromacs simulation one should use mdrun with an extra -plumed flag. The flag can be used to specify the name of the PLUMED input file, e.g.:

gmx mdrun -plumed plumed.dat

For more information on gromacs you should visit http://www.gromacs.org