A basic PLUMED interface is already present in GROMACS

This patch previes extra features to be implemented in the official PLUMED integration in the next GROMACS version

Patching must be done in the gromacs root directory before the cmake command is invoked.

The GROMACS integration has some improvements with the compatibility wiht the multi-threading implementation but it is still preferable to configure gromacs as

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

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