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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

M. J. Harvey, G. Giupponi, G. De Fabritiis
Information and Communications Technologies, Imperial College London, South Kensington, London, SW7 2AZ, UK
Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639.

@article{harvey2009acemd,

   title={ACEMD: accelerating biomolecular dynamics in the microsecond time scale},

   author={Harvey, MJ and Giupponi, G. and Fabritiis, G.D.},

   journal={Journal of Chemical Theory and Computation},

   volume={5},

   number={6},

   pages={1632–1639},

   year={2009},

   publisher={ACS Publications}

}

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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.
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