High Performance Molecular Dynamics Simulations with FPGA Coprocessors*

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. Here we report on an implementation that we believe to be the first to combine a high-level of FPGA-specific design, systematically determined precision, hardware support for complex force models, and support for simulations of over 250K 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; a novel arithmetic mode; and restructurings of algorithms, e.g., multigrid, to map efficiently to FPGA resources. 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.