NAMD: Biomolecular Simulation on Thousands of Processors

J.C. Phillips, Gengbin Zheng, S. Kumar, L.V. Kale
2002 ACM/IEEE SC 2002 Conference (SC'02)  
NAMD is a parallel, object-oriented molecular dynamics program designed for high performance simulation of large biomolecular systems. NAMD employs the prioritized message-driven execution capabilities of the Charm++/Converse parallel runtime system, allowing excellent parallel scaling on both massively parallel supercomputers and commodity workstation clusters. This paper discusses the techniques which have allowed NAMD to effectively employ over one thousand processors in production simulations of biomedical relevance.
doi:10.1109/sc.2002.10019 dblp:conf/sc/PhillipsZKK02 fatcat:slik5zdeqvbzpm6h4722seroku