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NAnoscale Molecular Dynamics (NAMD)
| Laxmikant Kale | Abhinav Bhatele | Eric Bohm | James Phillips
Encyclopedia of Parallel Computing 2011
Publication Type: Paper
Repository URL: papers/EncyParComp
Abstract
NAMD (NAnoscale Molecular Dynamics, http://www.ks.uiuc.edu/Research/namd) is a parallel molecular dynamics (MD) code designed for high performance simulation of large biomolecular systems. Typical NAMD simulations include all-atom models of proteins, lipids, and/or nucleic acids as well as explicit solvent (water and ions) and range in size from 10,000 to 10,000,000 atoms. NAMD employs the prioritized message-driven execution capabilities of the Charm++ parallel runtime system (http://charm.cs.uiuc.edu), allowing excellent parallel scaling on both massively parallel supercomputers and commodity workstation clusters. NAMD is distributed free of charge as both source code and pre-compiled binaries by the Theoretical and Computational Biophysics Group (http://www.ks.uiuc.edu) of the University of Illinois Beckman Institute. NAMD development is primarily funded by the NIH through the Resource for Macromolecular Modeling and Bioinformatics. NAMD has been downloaded by over 36,000 registered users, over 8,000 of whom have downloaded multiple releases.
TextRef
Laxmikant V. Kale, Abhinav Bhatele, Eric J. Bohm, James C. Phillips, NAnoscale Molecular Dynamics (NAMD), Encyclopedia of Parallel Computing, David Padua, Ed., 2011 (to appear)
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