Definition
NAMD is a parallel molecular dynamics software for biomolecular simulations.
Discussion
Introduction
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 [1–4]. 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++/Converse parallel runtime system (http://charm.cs.illinois.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...
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Kalé, L.V., Bhatele, A., Bohm, E.J., Phillips, J.C. (2011). NAMD (NAnoscale Molecular Dynamics). In: Padua, D. (eds) Encyclopedia of Parallel Computing. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-09766-4_505
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DOI: https://doi.org/10.1007/978-0-387-09766-4_505
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-09765-7
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