NAMD

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Running NAMD on Ares the Linux cluster:

This sample LSF job script(lsf-job-script.txt) will run NAMD over gigabit on the cluster:

#!/bin/bash
#BSUB -J namd_test
#BSUB -q ccs_low
#BSUB -W 23:00
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -n 8

#set nodelist file
export nodelistfile="nodelist.txt"
echo "group main"> $nodelistfile

for host in $LSB_HOSTS ; do
host=`echo $host|awk -F. '{print $1}'`
echo "host $host">> $nodelistfile
done

#get the number of nodes we are going to use
export tmp_num_procs=`cat ./$nodelistfile |wc -l`
export num_procs=`expr $tmp_num_procs - 1`

export CONV_RSH=ssh
export CONF=equil_0300
export P4_GLOBMEMSIZE=8000000
export BINDIR=/usr/local/opt/NAMD/NAMD_2.6_Linux-amd64-TCP
############ THE JOB ITSELF #############################


echo Start Job
date
pwd

$BINDIR/charmrun ++p $num_procs ++nodelist $nodelistfile $BINDIR/namd2 $CONF.conf > $CONF.out

echo End Job
#################################################

Submit your NAMD job to the queuing system:
```
 >>bsub < lsf-job-script.txt
 
```

For more information on using the LSF queuing system go here.