On September 22nd, OSC switched to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.


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 and Restrictions


The following versions of NAMD are available:

Version Ruby Owens Pitzer
2.11   X  
2.12 X* X  
2.13b2     X
2.13   X* X*
* Current default version
*  IMPORTANT NOTE: You need to load correct compiler and MPI modules before you use NAMD. In order to find out what modules you need, use module spider namd/{version} .

You can use  module spider namd  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


NAMD is available to all OSC users for academic purpose.

Publisher/Vendor/Repository and License Type

TCBG, University of Illinois/ Open source (academic)



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:


The simple batch script for Owens below demonstrates some important points. It requests 56 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=28
#PBS -l walltime=2:00:00
#PBS -S /bin/bash
#PBS -j oe
module load namd
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
pbsdcp -p apoa1.namd apoa1.pdb apoa1.psf *.xplor $TMPDIR
# Use TMPDIR for best performance.
run_namd apoa1.namd
pbsdcp -g '*' $PBS_O_WORKDIR
NOTE: ppn should be 20 on Ruby and 40 on Pitzer.

GPU support

We have GPU support with NAMD 2.12 for Owens and Ruby clusters. These temporarily use pre-compiled binaries due to installation issues.  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

Further Reading