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NAMD

Introduction

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, 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. Additional information can be found at: NAMD - Scalable Molecular Dynamics

Version

Version 2.6 is currently available at OSC.

Availability

NAMD is available on the Glenn Cluster and the BALE Cluster.

Usage

Users are not required to complete a license agreement.

Execution

On each Cluster, NAMD is accessed by executing the following command:

module load namd

Below is a sample batch script for the Glenn Cluster. It asks for 8 processors and 2 hours of walltime. If the job goes beyond 2 hours, the job would be terminated.

#PBS -N apoa1
#PBS -l nodes=2:ppn=4
#PBS -l walltime=2:00:00
#PBS -S /bin/bash
#PBS -j oe

module load namd
cd $PBS_O_WORKDIR
pbsdcp apoa1.namd apoa1.pdb apoa1.psf *.xplor $TMPDIR
cd $TMPDIR
run_namd apoa1.namd
pbsdcp -g '*' $PBS_O_WORKDIR

Documentation

General documentation is available at NAMD - Scalable Molecular Dynamics