Amber PME Molecular Dynamics Optimization

This chapter presents an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, which forms part of the Amber v14 MD software package, which makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct space summation and neighbor list build to the coprocessor. The modified algorithm provides performance improvement for large systems (~ 1 million atoms), achieving a 1.62× performance improvement from the baseline implementation for satellite tobacco mosaic virus when executed on Xeon + Xeon Phi comparing to Xeon-only code. It is our belief that Amber is one of the first MD packages to publish official support for PME MD simulations, in production software, on an Intel Xeon Phi coprocessor by offloading portions of work. We also present various algorithm optimizations, code optimizations, and load balance modifications to get the maximum performance from Xeon and Xeon Phi while not impacting simulation accuracy.