NAnoscale Molecular Dynamics (NAMD)
Encyclopedia of Parallel Computing 2011
Publication Type: Paper
Repository URL: papers/EncyParComp
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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)
People
- Laxmikant Kale
- Abhinav Bhatele
- Eric Bohm
- James Phillips
Research Areas