ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale

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dc.creatorHarvey, M. J.
dc.creatorGiupponi, G.
dc.creatorDe Fabritiis, G.
dc.date2009-02-05
dc.date.accessioned2026-07-07T12:38:11Z
dc.date.available2026-07-07T12:38:11Z
dc.descriptionThe 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 bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also 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. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.
dc.identifierhttps://arxiv.org/abs/0902.0827
dc.identifierhttp://arxiv.org/abs/0902.0827
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/218668
dc.subjectComputational Physics
dc.subjectBiological Physics
dc.titleACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale
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