If you would like to try running gromacs on the gpu please take a look at this.

There are many different versions of gromacs, to see what's available try:

user@login01:~ $ qsub my_job.msub

my_job.msub

#!/bin/bash
#PBS -l select=10:ncpus=8:mpiprocs=8:jobtype=nehalem,place=excl
#PBS -l walltime=00:40:00
#PBS -q workq
#PBS -M user@someinstitution.ac.za
#PBS -m be
#PBS -V
#PBS -e /export/home/user/scratch5/gromacs_data/std_err.txt
#PBS -o /export/home/user/scratch5/gromacs_data/std_out.txt
#PBS -N GROMACS_JOB
#PBS -mb
 
MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH
source /etc/profile.d/modules.sh
 
#######module add
module add gromacs/4.6.1_nehalem
 
NP=`cat ${PBS_NODEFILE} | wc -l`
 
EXE="mdrun_mpi"
ARGS="-s XXX -deffnm YYYY"
 
cd /export/home/user/scratch5/gromacs_data
mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}

Finally submit your job using:

user@login01:~ $ qsub my_job.msub