NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.

Availability & Restrictions

NAMD is available without restriction to all OSC users.

The following versions of NAMD are available:

Version Glenn Oakley
2.6 X  
2.7 X  
2.9   X

Usage

Set-up

To load the NAMD software on the Glenn system, use the following command:

module load namd-2.6-mpi

Using NAMD

NAMD is rarely executed interactively because preparation for simulations is typically performed with extraneous tools, such as, VMD.

Batch Usage

Sample batch scripts and input files are available here:

/nfs/10/srb/workshops/compchem/namd/

The simple batch script below demonstrates the important points. It requests 16 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=8
#PBS -l walltime=2:00:00
#PBS -S /bin/bash
#PBS -j oe

module load namd-2.6-mpi
cd $PBS_O_WORKDIR
pbsdcp -p apoa1.namd apoa1.pdb apoa1.psf *.xplor $TMPDIR
cd $TMPDIR
run_namd apoa1.namd
pbsdcp -pg '*' $PBS_O_WORKDIR

Further Reading

Supercomputer: 
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