Compiled hardware acceleration of Molecular Dynamics code

Abstract

The objective of molecular dynamics (MD) simulations is to determine the shape of a molecule in a given biomolecular environment. These simulations are very demanding computationally, where simulations of a few milliseconds can take days or months depending on the number of atoms involved. Therefore, MD simulations are a prime candidate for FPGA-based code acceleration. We have investigated the possible acceleration of the commonly used MD program NAMD. This code is highly optimized for software based execution and does not benefit from an FPGA-based acceleration as written. We have therefore developed a modified version, based on the calculations NAMD performs, that streams a set of data through a highly pipelined circuit on the FPGA. We have used the ROCCC compiler toolset to generate the circuit and implemented it on the SGI Altix 4700 fitted with a RASC RC100 blade.