The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein–protein and protein–lipid interactions and material science applications as ionic liquids and aedamers.
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Force-field parameters and procedures (for example, tutorials) are publicly available at http://cgmartini.nl. Simulation data (for example, trajectories) supporting the results of this paper are available from the corresponding authors upon reasonable request.
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We thank all members of the S.J.M. group and also external users for testing Martini 3 in its open-beta version. In particular, we thank C. F. E. Schroer, P. W. J. M. Frederix, W. Pezeshkian, M. N. Melo, H. I. Ingólfsson, M. Tsanai, M. König, P. A. Vainikka, T. Zijp, L. Gaifas, J. H. van der Woude, M. Espinoza Cangahuala, M. Scharte, J. Cruiming, L. M. van der Sleen, V. Verduijn, A. H. Beck Frederiksen, B. Schiøtt, M. Sikora, P. Schmalhorst, R. A. Moreira, A. B. Poma, K. Pluhackova, C. Arnarez, C. A. López, E. Jefferys and M. S. P. Sansom for their preliminary tests with a lot of different systems including aedamers, sugars, amino acids, deep eutectic solvents, lipids, peptides and proteins. We also thank the Center for Information Technology of the University of Groningen for providing access to the Peregrine high-performance computing cluster. We acknowledge the National Computing Facilities Foundation of The Netherlands Organization for Scientific Research (NWO), CSC–IT Center for Science Ltd (Espoo, Finland) and CINES (France) for providing computing time. Work in the S.J.M. group was supported by an European Research Council advanced grant no. ‘COMP-MICR-CROW-MEM’. R.A. thanks the NWO (Graduate Programme Advanced Materials, no. 022.005.006) for financial support. L.M. acknowledges the Institut National de la Santé et de la Recherche Medicale and the Agence Nationale de la Recherche for funding (grant no. ANR-17-CE11-0003) and GENCI-CINES for computing time (grant no. A0060710138). S.T. acknowledges the support from the European Commission via a Marie Skłodowska-Curie Actions individual fellowship (MicroMod-PSII, grant agreement no. 748895). M.J. thanks the Emil Aaltonen foundation for financial support. I.V. thanks the Academy of Finland (Center of Excellence program (grant no. 307415)), Sigrid Juselius Foundation, the Helsinki Institute of Life Science fellow program and the HFSP (research grant no. RGP0059/2019). R.B.B. and J.D. were supported by the intramural research program of the NIDDK, NIH. Their work used the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov). H.M.-S. acknowledges the Czech Science Foundation (grant no. 19-19561S). J.B. acknowledges funding from the TOP grant from S.J.M. (NWO) and the EPSRC program grant no. EP/P021123/1. Work in D.P.T.’s group is supported by the Natural Sciences and Engineering Research Council (Canada) and Compute Canada, funded by the Canada Foundation for Innovation. D.P.T. acknowledges further support from the Canada Research Chairs program. N.R. acknowledges funding from the Norwegian Research Council (FRIMEDBIO nos. 251247 and 288008) and computational resources from UNINETT SIGMA2 AS (grant no. NN4700K). H.M.K. acknowledges funding from the University of Calgary through the ‘Eyes High Postdoctoral Fellowship’ program.
The authors declare no competing interests.
Peer review information Nature Methods thanks the anonymous reviewers for their contribution for the peer review of this work. Arunima Singh was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
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Souza, P.C.T., Alessandri, R., Barnoud, J. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 18, 382–388 (2021). https://doi.org/10.1038/s41592-021-01098-3
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