Preliminary report: FPGA acceleration of molecular dynamics computations

Molecular dynamics (MD) is of central importance to computational chemistry and its myriad applications. In this paper we show that, at even a preliminary stage of development, MD can be implemented efficiently on a COTS FPGA board, and that a 57x speed-up over a PC implementation can be obtained. We sketch our FPGA implementation and describe how performance tuning and precision management could double this factor.