Pittsburgh Supercomputing Center 

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PSCBridges

PSC Receives NSF Award for Bridges Supercomputer - Read More

#! /bin/csh 
#PBS -l ncpus=16
#PBS -l walltime=10:00
#PBS -j oe
#PBS -N desmond_dhfr
#PBS -o desmond_dhfr.out
#PBS -q debug

# set up the module command
source /usr/share/modules/init/csh

# load the boost and desmond modules
module load boost
module load desmond 

set echo

date

# Desmond will fail if the output directory already exists.
# create a unique directory for the job to run in using the PBS jobid

set JOBNO=`echo $PBS_JOBID | sed 's/.tg-login[0-9].blacklight.psc.teragrid.org//'`
set WORKDIR=${SCRATCH}/$JOBNO

# Make and then move to your working directory
mkdir $WORKDIR
cd $WORKDIR

mpirun -np $PBS_NCPUS dplace -s1 desmond  --include $DESMOND_HOME/share/samples/dhfr.cfg   --cfg boot.file=$DESMOND_HOME/share/samples/dhfr.dms   --cfg mdsim.plugin.eneseq.name=dhfr.eneseq  --destrier mpi