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 Oakley ruby Owens
2.9 X    
2.10

X

   
2.11 X   X
2.12 X* X* X*

 

*: Current default version

Set-up

To load the NAMD software on the system, use the following command: module load namd/"version"  where "version" is the version of NAMD you require. The following will load the default or latest version of NAMD:  module load namd  

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:

~srb/workshops/compchem/namd/

The simple batch script for Oakley below demonstrates some important points. It requests 24 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=12
#PBS -l walltime=2:00:00
#PBS -S /bin/bash
#PBS -j oe
module load namd
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
NOTE: ppn should =20 on Ruby and =28 on Owens.

GPU support

We have temporary GPU support with NAMD 2.12 for Owens and Ruby clusters, and with NAMD 2.11 for Oakley. For more detail, please read the corresponding example script:

~srb/workshops/compchem/namd/apoa1.namd212nativecuda.owens.pbs  # for Owens
~srb/workshops/compchem/namd/apoa1.namd212nativecuda.ruby.pbs   # for Ruby
~srb/workshops/compchem/namd/apoa1.namd211nativecuda.oakley.pbs  # for Oakley

Further Reading

Supercomputer: 
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