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Harvey, M. J; De Fabritiis, G
Journal of chemical theory and computation, 2009-Sep-08, Letnik: 5, Številka: 9Journal Article
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 and exhibits an accuracy comparable to that of a reference double-precision CPU implementation.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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