In order to use Gromacs append the following lines to your .profile file:

export MODULEPATH=/opt/gridware/applications/gromacs/modules:$MODULEPATH
module add gromacs/4.6.1 mpich2/1.5

To complete the setup log out of the cluster and back in again (or just source your .profile file) to update your environment variables.

The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts:

gromacs.job

#This job tests GROMACS, it requires the input file min.steep0.tpr to be in the working directory.
 
#MSUB -l nodes=2:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=24:00:00
#MSUB -j oe
#MSUB -o out.log
#MSUB -d /export/home/username/scratch5/gromacs
#MSUB -V
 
NP=`cat $PBS_NODEFILE | wc -l`
BIN=mdrun_mpi
ARGS="-s min.steep0.tpr -deffnm min.steep0 -npme 4"
 
mpirun -np $NP -machinefile $PBS_NODEFILE $BIN $ARGS

This job submission script requires that the file min.steep0.tpr be in the working directory specified above.

NOTE: Please ensure that all file I/O associated with your job only occurs in a sub-directory of your scratch5 partition.

Submit the job using the following command:

msub gromacs.job