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:

gromacs.job

#MSUB -l nodes=2:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=150:00:00
#MSUB -j oe
#MSUB -o out.log
#MSUB -d /export/home/username/scratch5/gromacs
#MSUB -V
 
#This job tests GROMACS, it requires the input file min.steep0.tpr to be in the same directory.
 
nproc=`cat $PBS_NODEFILE | wc -l`
echo $nproc
exe=mdrun_mpi
args="-s
min.steep0.tpr
-deffnm
min.steep0
-npme 4"
 
mpirun -np $nproc -machinefile $PBS_NODEFILE $exe $args > results.log

The submission script above requires that the file min.steep0.tpr is in the job working directory.