NAMD Molecular Dynamics
by the Theoretical and Computational Biophysics Group
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds
of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed
free of charge with source code.
Any reports or published results obtained with the Software will acknowledge its use by the appropriate citation as follows:
NAMD was developed by the Theoretical 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:
Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten.
NAMD2: Greater scalability for parallel molecular dynamics. J. Comp. Phys., 151:283-312, 1999.
Electronic documents will include a direct link to the official NAMD page:
http://www.ks.uiuc.edu/Research/namd/
One copy of each publication or report will be supplied to Illinois through Dr. Gila Budescu at the addresses listed below in Contact Information.
Running NAMD:
chmsgi and any SGI machine that is running IRIX 6.5 or later and has chmsgi:/chem mounted you will need to add the following alias to your .tcshrc file:
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