Integrating FPGA Acceleration into the Protomol Molecular Dynamics Code: Preliminary Report

The authors describe a new pipeline for computing non-bonded forces and its integration into the ProtoMol molecular dynamics (MD) code. There are several innovations: a novel interpolation strategy, including use of higher order terms; coefficient generation with orthonormal functions; the introduction of "semi-floating point" numbering; and various issues related to system integration. As a result, we are able to model far more particle types, without relying on complex buffering, and obtain higher accuracy than previously. A two pipeline accelerator has been implemented on a 2004-era Xilinx VirtexII Pro VP70, integrated into ProtoMol, and tested with an enzyme inhibitor model having 8000 particles and 26 particle types. Despite performing all O(n) work on the host PC, as well as the data conversion and communication overhead, this implementation yields 5.5x to 15.7x speed-ups over a 2.8GHz PC (depending on whether cell lists are used), and with accuracy comparable to the serial code