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


  • Vladimir A. Fedorov Lomonosov Moscow State University, Moscow
  • Ekaterina G. Kholina Lomonosov Moscow State University, Moscow
  • Ilya B. Kovalenko Lomonosov Moscow State University, Moscow Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow Astrakhan State University, Astrakhan Scientific and Technological Center of Unique Instrumentation of the RAS, Moscow Center for Theoretical Problems of Physicochemical Pharmacology, RAS, Moscow
  • Nikita B. Gudimchuk Lomonosov Moscow State University, Moscow Center for Theoretical Problems of Physicochemical Pharmacology, RAS, Moscow
  • Philipp S. Orekhov Lomonosov Moscow State University, Moscow Moscow Institute of Physics and Technology, Dolgoprudny
  • Artem A. Zhmurov KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm




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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How to Cite

Fedorov, V. A., Kholina, E. G., Kovalenko, I. B., Gudimchuk, N. B., Orekhov, P. S., & Zhmurov, A. A. (2021). Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions. Supercomputing Frontiers and Innovations, 7(4), 62–67. https://doi.org/10.14529/jsfi200405