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NAMD

NAMD is a popular molecular dynamics program. A parallel version of it is available on the MSG. A simple submit script for executing a copy of the 'alanin' example which comes with it is as follows. It uses the 'orte' parallel environment in place of the similar 'mpich' one so as to avail itself of the tighter SGE integration capabilities available in recent implementations of OpenMPI.


Categories for this software:Computational Chemistry
 What is NAMDNAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.

NAMD is developed by the University of Illinois.

How to useNAMD is free to use. The license is here http://www.ks.uiuc.edu/Research/namd/license.html

Sample Script

First copy input files to your working directory, as is described below.

NAMD example
#!/bin/sh
#$ -S /bin/sh
#$ -pe short 4
#$ -cwd
#

#
# first copy input files to your local dir
# cp  /opt/sw/namd-2.6a/src/alanin* .
#

module load namd
mpirun namd2 ./alanin

 

 

 


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