URL]. This work was supported in part by the National Institues

Y. Gu, T. VanCourt, M.C. Herbordt / MD with FPGAs / IEE-CDT-2006 1 Molecular Dynamics (MD) is of central importance to computational chemistry. Here we show that MD can be implemented efficiently on a COTS FPGA board, and that speed-ups from 31 × to 88 × over a PC implementation can be obtained. Although the amount of speed-up depends on the stability required, 46 × can be obtained with virtually no detriment, and the upper end of the range is apparently viable in many cases. We sketch our FPGA implementations and describe the effects of precision on the trade-off between performance and quality of the MD simulation.