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--- howto:bioinformatics:gromacs [2014/07/02 16:31]
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-====== Running Gromacs ======
-If you would like to try running gromacs on the gpu please take a look at [[howto:gpu_gromacs|this]].
-There are many different versions of gromacs, to see what's available try:<code bash>user@login01:~ $ qsub my_job.msub</code>
-===== Job script =====
-<file bash 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}
-</file>
-===== Submit your job =====
-Finally submit your job using:<code bash>user@login01:~ $ qsub my_job.msub</code>

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