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We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel\u2010MPI and Open\u2010MPI. The largest system showed near\u2010perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687\u2009ns\/d for the 82k atom system, 116\u2009ns\/d for the 53M atom system, and about 35\u2009ns\/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state\u2010of\u2010the\u2010art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.<\/jats:p>","DOI":"10.1002\/jcc.70059","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T12:10:46Z","timestamp":1739448646000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster"],"prefix":"10.1002","volume":"46","author":[{"given":"Carsten","family":"Kutzner","sequence":"first","affiliation":[{"name":"Theoretical and Computational Biophysics Max Planck Institute for Multidisciplinary Sciences  G\u00f6ttingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vedran","family":"Mileti\u0107","sequence":"additional","affiliation":[{"name":"Max Planck Computing and Data Facility  Garching Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Palacio Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Biophysics  Frankfurt am Main Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Rampp","sequence":"additional","affiliation":[{"name":"Max Planck Computing and Data Facility  Garching Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerhard","family":"Hummer","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Biophysics  Frankfurt am Main Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bert L.","family":"de Groot","sequence":"additional","affiliation":[{"name":"Theoretical and Computational Biophysics Max Planck Institute for Multidisciplinary Sciences  G\u00f6ttingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helmut","family":"Grubm\u00fcller","sequence":"additional","affiliation":[{"name":"Theoretical and Computational Biophysics Max Planck Institute for Multidisciplinary Sciences  G\u00f6ttingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,2,13]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-1394-8_18"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2024.102887"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.26450"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.3389\/fchem.2023.1106495"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1080\/08927029008022127"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20289"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1121"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2021.108171"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21287"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.3c06662"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-15976-8_1"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-86359-3_21"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2014.06.004"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00744"},{"key":"e_1_2_8_17_1","unstructured":"Max Planck Computing and Data Facility \u201cViper User Guide \u201dhttps:\/\/docs.mpcdf.mpg.de\/doc\/computing\/viper\u2010user\u2010guide.html."},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1066115"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2690"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2012.02.004"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abm9506"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-111622-091147"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd9776"},{"key":"e_1_2_8_24_1","article-title":"Nuclear Pores as Conduits for Fluid Flow During Osmotic Stress","author":"Hoffmann P. 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