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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

2009; American Chemical Society; Volume: 5; Issue: 6 Linguagem: Inglês

10.1021/ct9000685

1549-9626

M J Harvey, G. Giupponi, Gianni De Fabritiis,

RNA and protein synthesis mechanisms

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein systems with over 23 000 atoms. We provide a validation and performance evaluation of the code and run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. We believe that microsecond time scale molecular dynamics on cost-effective hardware will have important methodological and scientific implications.