2002 · 209 citations · 16 references
Natural SciencesBioinformaticsHigh-performance ComputingCluster ComputingComputational ChemistryParallel ComputingBiomolecular ElectrostaticsElectrostatic Interactions In BiomoleculesElectrostatics In BiomoleculesMolecular DynamicsMolecular SimulationParticle-based SimulationBiomolecular SimulationHigh-performance Computing PerformanceLatency ToleranceMolecular Simulation AlgorithmsPredictive Load BalancingScalabilitySpatial DecompositionStrong Scalability
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. 1
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