NAMD

General Information

Short Description: NAMD is a parallel molecular dynamics code designed for high-performance simulationsof large bimolecular systems

Category: Computational Chemistry

Installation Information

Version: 2.6     Version Date:  August, 2006

Technical support:  Please contact Research Services (researchservices@bc.edu)

Terms of Use:  

License Information

Number of Licenses:  Licensed for use on the Scorpio Linux Cluster.

Type of License:  Network

Installed Sites: Scorpio Linux Cluster.

Installed Platforms: Linux

Vendor/Developer:  Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign

Vendor Website:  www.ks.uiuc.edu/Research/namd

Usage Information

To use interactively, first load the namd module by typing:

    module load namd

To use NAMD with PBS, create a file called namd.pbs that contains:

#!/bin/tcsh
#PBS -l mem= 2gb,nodes=1:ppn=4,walltime=75:00:00

cd directory-that-contains-your-namd-script
./namd_script input.inp

The above will request 4 processors and 2 GB of memory on one node, and 75 hours of time.  Use your input file instead of "input.inp".

You also need to create a file called namd_script with the following:

#!/bin/sh
/usr/public/Modules/3.2.3/init/sh
module load namd

# create node-list file
rm -rf $HOME/.mpd.host.*
NODELIST="$HOME/.mpd.host.$LSB_JOBID"
# use ssh instead of rsh
export CONV_RSH=ssh

output=`echo $LSB_MCPU_HOSTS | /bin/awk '
    BEGIN {counter1=0;counter2=0}
    {
      size = split($0, a, " ");
      for (i = 1; i <= size; i += 2) {
        counter1 = counter1 + 1;
        counter2 = counter2 + a[i + 1];
        for (j = 0; j < a[i + 1]; ++j) {
            print "host", a[i] > hfile;
        }
      }
    }
   END {print counter2}' hfile=$NODELIST`

# find full path of namd2
command=`which namd2`

echo "charmrun ++p $TOTAL_NUM_PROC ++nodelist $NODELIST namd2 $@"

charmrun ++p $output ++nodelist $NODELIST $command $@

 To submit a job to the queues, type:

qsub namd.pbs

Documentation

 For information about namd see www.ks.uiuc.edu/Research/namd