namd


Introduction:

NAMD is a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems. NAMD is
distributed free of charge and includes source code. It was developed by
the University of Illinois at Urbana-Champaign.

NAMD scales to hundreds of processors on high-end parallel platforms,
as well as tens of processors on low-cost commodity clusters, and also
runs on individual desktop and laptop computers. NAMD works with AMBER
and CHARMM potential functions, parameters, and file formats.

Web site:


http://www.ks.uiuc.edu/Research/namd/

Reference:

Usage:

On any ARC cluster, check the installation details
by typing “module spider namd”.

NAMD requires that the appropriate modules be loaded before it can be run.
One version of the appropriate commands for use on NewRiver is:

module purge
module load gcc/4.7.2
module load openmpi/1.8.5
module load namd/2.10
    

The builds that are provided on ARC clusters support the InfiniBand network
through the ibverbs interface. NAMD uses charm++ parallel objects for
parallelization and the program launch uses the charmrun interface, as in

      charmrun namd2 +p<procs> <configfile>
    

Examples:

A sample problem shows how to solvate a protein (ubiquitin) in a box of water.
The example includes the following files:

  • par_all27_prot_lipid.inp
  • ubq_wb.pdb
  • ubq_wb.psf
  • ubq_wb_eq.conf

Here is a sample bash script to run this example on NewRiver:

#! /bin/bash
#
#PBS -l nodes=2:ppn=24
#PBS -l walltime=00:05:00
#PBS -W group_list=newriver
#PBS -q open_q
#PBS -j oe
#
cd $PBS_O_WORKDIR
#
module purge
module load gcc/4.7.2
module load openmpi/1.8.5
module load namd/2.10
#
charmrun namd2 +p$PBS_NP ubq_wb_eq.conf

A complete set of files to carry out a similar process are available in
namd_example.tar.gz