Bonded Force Computations on FPGAs

Abstract

While acceleration of Molecular Dynamics has received much attention, a significant part of that application, the bonded force calculation, has not. We present what we believe to be the first description and analysis of bonded force calculations outside of ASICs. We characterize the computational requirements. We find that a naive direct implementation requires FPGA resources out of proportion with its proportion of the workload. We investigate other options including various softcores and speed/area tradeoffs. These result in an assortment of solutions optimal for various combinations of problem and cluster size.