Encyclopedia of Parallel Computing

2011 Edition
| Editors: David Padua

NAMD (NAnoscale Molecular Dynamics)

  • Laxmikant V. Kalé
  • Abhinav Bhatele
  • Eric J. Bohm
  • James C. Phillips
Reference work entry
DOI: https://doi.org/10.1007/978-0-387-09766-4_505

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, 2, 3, 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...

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Bibliography

  1. 1.
    Bhatele A, Kumar S, Mei C, Phillips JC, Zheng G, Kalè LV (2008) Overcoming scaling challenges in biomolecular simulations across multiple platforms. In: Proceedings of IEEE international parallel and distributed processing symposium, Miami, 2008Google Scholar
  2. 2.
    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalè LV, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781–1802Google Scholar
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    Phillips JC, Zheng G, Kumar S, Kale LV (2002) NAMD: biomolecular simulation on thousands of processors. In: Proceedings of the 2002 ACM/IEEE conference on supercomputing, pp 1–18, Baltimore, 2002Google Scholar
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    Kalè LV, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips JC, Shinozaki A, Varadarajan K, Schulten K (1999) NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 151:283–312zbMATHGoogle Scholar
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    Plimpton SJ, Hendrickson BA (1996) A new parallel method for molecular-dynamics simulation of macromolecular systems. J Comp Chem 17:326–337Google Scholar
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    Kalè LV, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips JC, Shinozaki A, Varadarajan K, Schulten K (1998) NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys 151:283–312, 1999Google Scholar
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    Snir M (2004) A note on n-body computations with cutoffs. Theory Comput Syst 37:295–318zbMATHMathSciNetGoogle Scholar
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    Bhatelè A, Kalè LV, Kumar S (2009) Dynamic topology aware load balancing algorithms for molecular dynamics applications. In: 23rd ACM international conference on supercomputing, Yorktown Heights, 2009Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Laxmikant V. Kalé
    • 1
  • Abhinav Bhatele
    • 1
  • Eric J. Bohm
    • 1
  • James C. Phillips
    • 1
  1. 1.Department of Computer ScienceUniversity of Illinois at Urbana-ChampaignUrbanaUSA