NAMD (NAnoscale Molecular Dynamics)
NAMD is a parallel molecular dynamics software for biomolecular simulations.
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...
- 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.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
- 3.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
- 5.Plimpton SJ, Hendrickson BA (1996) A new parallel method for molecular-dynamics simulation of macromolecular systems. J Comp Chem 17:326–337Google Scholar
- 6.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
- 8.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