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arXiv · 0902.0827

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

M. J. Harvey·G. Giupponi·G. De Fabritiis
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Abstract

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 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.

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M. J. Harvey, G. Giupponi, G. De Fabritiis. 2009-02-05. ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale. https://arxiv.org/abs/0902.0827

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