A Practical Guide to the Best Hardware for Molecular Dynamics Simulations: A Comparison of Molecular Dynamics Software Performance Using the Gromacs Package as an Example

Abstract

Our comparative performance analysis of molecular dynamics software (using the popular GROMACS package as an example) provides the guidelines for selection of the best-performing GPU-based architectures for both all-atom and coarse-grained MD simulations of realistic molecular systems. It also outlines certain limitations of the single-node workstations and highlights the importance of the HPC platforms (e.g., “Lomonosov-2” supercomputer) for the simulations of large systems exceeding ca. 200,000 particles on the relevant time scale. These data can be used as the practical guidelines for choosing optimal hardware for molecular dynamics simulations.