An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
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DOI：
10.1021/ct900275y
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发表时间：
2009-09-01
影响因子：
5.5
通讯作者：
De Fabritiis, G.
中科院分区：
文献类型：
--
作者：
Harvey, M. J.;De Fabritiis, G.
光滑粒子网格Ewald求和方法被广泛用于有效地计算分子动力学模拟中的长程静电力项，并且在为各种并行计算机架构开发优化实现方面已经做了大量工作。我们描述了Nvidia图形处理单元（GPU）的实现，这些GPU是具有高度内在并行性和算术性能的通用计算设备。我们发现，对于典型的生物分子模拟（例如，DHFR，26 K原子），一个配备GPU的工作站能够提供足够的性能，以允许模拟速率接近50 ns/天，当与ACEMD分子动力学包（1）结合使用时，并表现出与参考双精度CPU实现的精度相当的精度，
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 approximate to 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,