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An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
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    An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
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    High Performance Computing Service, Information and Communications Technologies, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom and Computational Biochemistry and Biophysics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain
    * Corresponding authors. E-mail: [email protected] and [email protected].
    †Imperial College London.
    ‡Universitat Pompeu Fabra.
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2009, 5, 9, 2371–2377
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    https://doi.org/10.1021/ct900275y
    Published August 14, 2009
    Copyright © 2009 American Chemical Society

    Abstract

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    The smooth particle mesh Ewald summation method is widely used to efficiently compute long-range electrostatic force terms in molecular dynamics simulations, and there has been considerable work in developing optimized implementations for a variety of parallel computer architectures. We describe an implementation for Nvidia graphical processing units (GPUs) which are general purpose computing devices with a high degree of intrinsic parallelism and arithmetic performance. We find that, for typical biomolecular simulations (e.g., DHFR, 26K atoms), a single GPU equipped workstation is able to provide sufficient performance to permit simulation rates of ≈50 ns/day when used in conjunction with the ACEMD molecular dynamics package (1) and exhibits an accuracy comparable to that of a reference double-precision CPU implementation.

    Copyright © 2009 American Chemical Society

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    Cite this: J. Chem. Theory Comput. 2009, 5, 9, 2371–2377
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    Published August 14, 2009
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