The grid inhomogeneous solvation theory (GIST) method requires the often time-consuming calculation of water-water and water-solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP, GPUs, and particle mesh Ewald. This article details how the speed of this calculation can be increased by parallelizing it with MPI, where trajectory frames are divided among multiple processors. This requires very little communication between individual processes during trajectory processing, meaning the calculation scales well to large processor counts. This article also details how the entropy calculation, which must happen after trajectory processing since it requires information from all trajectory frames, is parallelized via MPI. This parallelized GIST method has been implemented in the freely-available CPPTRAJ analysis software.
Keywords: GIST; molecular dynamics; parallel analysis; trajectory analysis.
Published 2023. This article is a U.S. Government work and is in the public domain in the USA.