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NAMD

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is file-compatible with AMBER, CHARMM and X-PLOR.

NAMD is licensed software from the University of Illinois. Please read and follow the terms of the license agreement.

Sample scripts for NAMD use are available in directory /opt/packages/examples/namd on Bridges and Bridges-2.

Documentation

  • NAMD web site
  • Example scripts:  For best performance, please see the  optimized example scripts for NAMD on Bridges  and Bridges-2 in directory /opt/packages/examples/namd.

Citations

Any reports or published results obtained with NAMD must acknowledge its use by the appropriate citation as follows:

“NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.”

Any published work which utilizes NAMD shall include the following reference:

“James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Scalable molecular dynamics on CPU and GPU architectures with NAMD. Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475”

Electronic documents will include a direct link to the official NAMD page at http://www.ks.uiuc.edu/Research/namd/

Usage on Bridges-2

Using the GPU-shared partition

When running a job in the GPU-shared partition, you must pass the numbers of the cpus assigned to your job to NAMD. If you do not, the job will fail. For the correct commands to do this, please see the example job in /opt/packages/examples/namd/GPU-shared.

General use

Please see the optimized example scripts in directory /opt/packages/examples/namd.

To see what versions of NAMD are available and if there is more than one, which is the default, along with some help, type

module spider namd

To use NAMD, include a command like this in your batch script or interactive session to load the NAMD module: (note ‘module load’ is case-sensitive):

module load namd

Usage on Bridges

To see what versions of NAMD are available type

module avail namd

To see what other modules are needed, what commands are available and how to get additional help type

module help namd

To use NAMD, include a command like this in your batch script to load the NAMD module:

module load namd

Be sure you also load any other modules needed, as listed by the module help namd command.