NAMD: Biomolecular simulation on thousands of processors

NAMD is a parallel, object-oriented molecular dynamics program designed for high perfor-mance 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.