Paper Citing NAMD - Abstract
Harvey, M. J.; De Fabritiis, G.
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2371-2377, SEP 2009
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,
