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 Oakley ruby Owens pitzer
2.9 X      


2.11 X   X  
2.12  X* X*  X*  
2.13b2       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 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
pbsdcp -p apoa1.namd apoa1.pdb apoa1.psf *.xplor $TMPDIR
run_namd apoa1.namd
pbsdcp -pg '*' $PBS_O_WORKDIR
NOTE: ppn should =20 on Ruby and =28 on Owens.

GPU support

We have GPU support with NAMD 2.12 for Owens and Ruby clusters, and with NAMD 2.11 for Oakley. 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
~srb/workshops/compchem/namd/apoa1.namd211nativecuda.oakley.pbs  # for Oakley

Further Reading