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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, 2008
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):1781–1802
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, 2002
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 151:283–312
Plimpton SJ, Hendrickson BA (1996) A new parallel method for molecular-dynamics simulation of macromolecular systems. J Comp Chem 17:326–337
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, 1999
Snir M (2004) A note on n-body computations with cutoffs. Theory Comput Syst 37:295–318
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, 2009
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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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