Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

Yongfeng Gu, Tom VanCourt, Martin C. Herbordt
2008 Parallel Computing  
FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There
more » ... several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.
doi:10.1016/j.parco.2008.01.007 pmid:19412319 pmcid:PMC2440579 fatcat:foc7lpzgafbrfmxn2bcr5h3td4