Adding PLUMED 2 Plugin to Gromacs 5.0.x

These instructions assume that you have downloaded your own copy of the Gromacs source code and unpacked it to a directory identified by the environment variable $GROMACS_TOP. e.g. for the central installation:

export GROMACS_TOP=/work/y07/y07/gmx/5.0.5-phase2-plumed/source

To add PLUMED to Gromacs $GROMACS_TOP must be on the /work filesystem. This is because the MPI version of PLUMED must be used to patch the Gromacs source code and MPI PLUMED will ony run on the compute nodes. As only /work is mounted on the compute nodes, the files to be patched must be on /work also.

As you must run the patch command on the compute nodes, you must run this from within an interactive job. Submit an interactve job on the short queue with (replacing "budget" with your project code):

qsub -IVl select=1,walltime=0:20:0 -q short -A budget

(please note the short queue is only available between 0900 and 1700, Monday to Fridays.) Wait for the job to start. Once it has started move to the GROMACS_TOP directory:

cd $GROMACS_TOP

Setup your environment to patch Gromacs using PLUMED:

module swap PrgEnv-cray PrgEnv-gnu
module load plumed2/2.1.2-gnu

You must set $TMPDIR to point to a location on /work so that the plumed executable can create files:

export TMPDIR=/work/y07/y07/gmx

Apply the PLUMED patch to Gromacs

aprun -n 1 plumed-mpi patch -p

Select the option for Gromacs 5. Once the patch has been applied, finish the interactive job:

exit

Now that Gromacs has been patched, you should rebuild it by following the build instructions for ARCHER.