job.pbs

>#!/bin/bash 
#PBS -V

### Job name
#PBS -N lumExp
#PBS -l walltime=02:00:00
#PBS -l nodes=8:ppn=8
#PBS -j oe
#PBS -S /bin/bash
#PBS -N test
#PBS -m e




## load modules for MD simulations
module load fftw3
module load gromacs-4.5.5
PBS_O_WORKDIR=/nfs/01/cwr0351/test
cd $PBS_O_WORKDIR




 ## copy files to the temporary folders
 pbsdcp *.* $TMPDIR
 cd $TMPDIR




 ## run gromacs command for MD
 grompp -f grompp.mdp -p topol.top -n index.ndx -c cg192x50a_NVT_503_md65.em.gro
 mdrun -s topol.tpr



 ## copy back files to the local directory
 pbsdcp -g ener.edr md.log traj.xtc state.cpt state_prev.cpt traj.trr $PBS_O_WORKDIR