An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
High Performance Computing Service, Information and Communications Technologies, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2371-2377.
@article{harvey2009implementation,
title={An implementation of the smooth particle mesh ewald method on gpu hardware},
author={Harvey, MJ and De Fabritiis, G.},
journal={Journal of Chemical Theory and Computation},
volume={5},
number={9},
pages={2371–2377},
year={2009},
publisher={ACS Publications}
}
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.
October 28, 2010 by hgpu
