OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Author:

Eastman Peter1ORCID,Galvelis Raimondas23ORCID,Peláez Raúl P.3ORCID,Abreu Charlles R. A.45ORCID,Farr Stephen E.6,Gallicchio Emilio78ORCID,Gorenko Anton9,Henry Michael M.10,Hu Frank1,Huang Jing11ORCID,Krämer Andreas12ORCID,Michel Julien6ORCID,Mitchell Joshua A.13,Pande Vijay S.1415,Rodrigues João PGLM15ORCID,Rodriguez-Guerra Jaime16ORCID,Simmonett Andrew C.17ORCID,Singh Sukrit10,Swails Jason18,Turner Philip19,Wang Yuanqing20,Zhang Ivy1021ORCID,Chodera John D.10ORCID,De Fabritiis Gianni2322ORCID,Markland Thomas E.1ORCID

Affiliation:

1. Department of Chemistry, Stanford University, Stanford, California 94305, United States

2. Acellera Laboratories, C Dr Trueta 183, 08005 Barcelona, Spain

3. Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C Dr. Aiguader 88, 08003 Barcelona, Spain

4. Chemical Engineering Department, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 68542, Brazil

5. Redesign Science Inc., 180 Varick St., New York, New York 10014, United States

6. EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom

7. Department of Chemistry and Biochemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210-2889, United States

8. Ph.D. Program in Chemistry and Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States

9. Stream HPC, Koningin Wilhelminaplein 1−40601, 1062 HG Amsterdam, Netherlands

10. Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York New York 10065, United States

11. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China

12. Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 12, 14195 Berlin, Germany

13. The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States

14. Andreessen Horowitz, 2865 Sand Hill Rd, Menlo Park, California 94025, United States

15. Department of Structural Biology, Stanford University, Stanford, California 94305, United States

16. Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics, Virchowweg 6, 10117 Berlin, Germany

17. Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States

18. Entos Inc., 9310 Athena Circle, La Jolla, California 92037, United States

19. College of Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States

20. Simons Center for Computational Physical Chemistry and Center for Data Science, New York University, 24 Waverly Place, New York, New York 10004, United States

21. Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States

22. ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain

Funder

Engineering and Physical Sciences Research Council

National Cancer Institute

Damon Runyon Cancer Research Foundation

Ministerio de Ciencia e Innovaci?n

National Heart, Lung, and Blood Institute

Memorial Sloan-Kettering Cancer Center

Chan Zuckerberg Initiative

Vir Biotechnology

Horizon 2020 Framework Programme

New York University

National Institute of General Medical Sciences

National Science Foundation

Publisher

American Chemical Society (ACS)

Subject

Materials Chemistry,Surfaces, Coatings and Films,Physical and Theoretical Chemistry

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