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.

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