Discrete Event Simulation of Molecular Dynamics with Configurable Logic

Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD). DMD uses simplified discretized models, enabling simulations to be advanced by event, with a resulting performance increase of several orders of magnitude. Even so, DMD is compute bound. Moreover, unlike MD, causality issues make DMD difficult to scale, with O(radicp) being the best so far achieved. We find that FPGAs are extremely well suited to accelerating DMD. The chaotic execution, which results in there being virtually no prediction window, is overcome with a long processing pipeline augmented with associative structures analogous to those used in CPU reorder buffers. Our primary result is a microarchitecture for DMD that processes events with a throughput equal to a small multiple of the FPGA´s clock, resulting in a hundred-fold speed-up over serial implementations.