Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations.

ABSTRACT: 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 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 simula

SUBMITTER: Gu Y 

PROVIDER: S-EPMC2440579 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature