Toward Large Scale Parallelization for Molecular Dynamics of Small Chemical Systems: A Combined Parallel Tempering and Domain Decomposition Approach

A combined parallel tempering (replica exchange) and domain decomposition approach is presented, which allows for the effective use of large numbers of processor cores (>256) on modest sized simulations of chemical systems (∼5000 sites). The approach is implemented in the gbmoldd molecular dynamics program for the simulation of coarse-grained molecular systems composed of combinations of isotropic and/or anisotropic particles. Benchmark results are presented for two test systems: a C24 united atom chain and a coarse-grained system of spherocylinders.