AMBER

Sample job file for running a Amber parallel job :

#!/bin/bash

#PBS -o logfile.log

#PBS -e errorfile.err

#PBS -l cput=120:00:00

#PBS -l select=2:ncpus=8

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

tempdir=$HOME/work/job$tpdir

mkdir -p $tempdir

cd $tempdir

cp -R $PBS_O_WORKDIR/* .

./run_MD

mv ../job$tpdir $PBS_O_WORKDIR/.

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