FPGA-based multigrid computations for molecular dynamics simulations

Abstract: FPGA-based acceleration of molecular dynam-ics (MD) has been the subject of several recent studies. Implementing long-range forces, however, has only re-cently been addressed. Here we describe a solution based on the multigrid method. We show that multigrid is, in general, an excellent match to FPGAs: the primary opera-tions take advantage of the large number of independently addressable RAMs and the efficiency with which complex systolic structures can be implemented. The multigrid ac-celerator has been integrated into our existing MD system, and an overall performance gain of 5x to 7x has been ob-tained, depending on hardware configuration and reference code. The simulation accuracy is comparable to the origi-nal double precision serial code. 1