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Gromacs

Sample job file for running a Gromacs job :

File Name : gromacs.cmd

#! /bin/bash

#PBS -l cput=02:00:00

#PBS -e errorfile.err

#PBS -o logfile.log

#PBS -l select=1:ncpus=1:ngpus=1

tpdir=`echo $PBS_JOBID | cut -f 1 -d .`

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

/gpuusers/sware/gromacs-gpu/bin/mdrun-gpu -s water.tpr -o water.trr -c water.out -g water.log

mv * $PBS_O_WORKDIR/.

rmdir $tempdir

In the command prompt, type the command, qsub gromacs.cmd