Published: 2021-02-10

Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions

Vladimir A. Fedorov, Ekaterina G. Kholina, Ilya B. Kovalenko, Nikita B. Gudimchuk, Philipp S. Orekhov, Artem A. Zhmurov


Molecular dynamics has proved itself as a powerful computer simulation method to study dynamics, conformational changes, and interactions of biological macromolecules and their complexes. In order to achieve the best performance and efficiency, it is crucial to benchmark various hardware platforms for the simulations of realistic biomolecular systems with different size and timescale. Here, we compare performance and scalability of a number of commercially available computing architectures using all-atom and coarse-grained molecular dynamics simulations of water and the Ndc80-microtubule protein complex in the GROMACS-2019.4 package. We report typical single-node performance of various combinations of modern CPUs and GPUs, as well as multiple-node performance of the “Lomonosov-2” supercomputer. These data can be used as the practical guidelines for choosing optimal hardware for molecular dynamics simulations.

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Publishing Center of South Ural State University (454080, Lenin prospekt, 76, Chelyabinsk, Russia)