title: An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.
abstract: 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.
authors.affiliation: 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.
authors.forename: M J
authors.initials: MJ
authors.lastname: Harvey
authors.affiliation: 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.
authors.forename: G
authors.initials: G
authors.lastname: De Fabritiis