Paper Citing NAMD - Abstract
Gu, Yongfeng; VanCourt, Tom; Herbordt, Martin C.
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
PARALLEL COMPUTING, 34:261-277, MAY 2008
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 256 K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are 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. (C) 2008 Elsevier B.V. All rights reserved.
