Martini 3: a general purpose force field for coarse-grained molecular dynamics

Paulo C.T. Souza; Riccardo Alessandri; Jonathan Barnoud; Sebastian Thallmair; Ignacio Faustino; Fabian Grünewald; Ilias Patmanidis; Haleh Abdizadeh; Bart M.H. Bruininks; Tsjerk A. Wassenaar; Peter C. Kroon; Josef Melcr; Vincent Nieto; Valentina Corradi; Hanif M. Khan; Jan Domański; Matti Javanainen; Hector Martinez-Seara; Nathalie Reuter; Robert B. Best; Ilpo Vattulainen; Luca Monticelli; Xavier Periole; D. Peter Tieleman; Alex H. de Vries; Siewert J. Marrink

doi:10.1038/s41592-021-01098-3

Martini 3: a general purpose force field for coarse-grained molecular dynamics

Paulo C.T. Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M.H. Bruininks, Tsjerk A. Wassenaar, Peter C. Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M. Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B. BestIlpo Vattulainen, Luca Monticelli, Xavier Periole, D. Peter Tieleman, Alex H. de Vries, Siewert J. Marrink

Physics

Research output: Contribution to journal › Article › Scientific › peer-review

624 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	382-388
Number of pages	7
Journal	Nature Methods
Volume	18
Issue number	4
DOIs	https://doi.org/10.1038/s41592-021-01098-3
Publication status	Published - Apr 2021
Publication type	A1 Journal article-refereed

Publication forum classification

Publication forum level 3

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-021-01098-3

http://hdl.handle.net/10138/334681

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Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., Kroon, P. C., Melcr, J., Nieto, V., Corradi, V., Khan, H. M., Domański, J., Javanainen, M., Martinez-Seara, H., Reuter, N., ... Marrink, S. J. (2021). Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods, 18(4), 382-388. https://doi.org/10.1038/s41592-021-01098-3

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title = "Martini 3: a general purpose force field for coarse-grained molecular dynamics",

abstract = "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.",

author = "Souza, {Paulo C.T.} and Riccardo Alessandri and Jonathan Barnoud and Sebastian Thallmair and Ignacio Faustino and Fabian Gr{\"u}newald and Ilias Patmanidis and Haleh Abdizadeh and Bruininks, {Bart M.H.} and Wassenaar, {Tsjerk A.} and Kroon, {Peter C.} and Josef Melcr and Vincent Nieto and Valentina Corradi and Khan, {Hanif M.} and Jan Doma{\'n}ski and Matti Javanainen and Hector Martinez-Seara and Nathalie Reuter and Best, {Robert B.} and Ilpo Vattulainen and Luca Monticelli and Xavier Periole and Tieleman, {D. Peter} and {de Vries}, {Alex H.} and Marrink, {Siewert J.}",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2021",

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doi = "10.1038/s41592-021-01098-3",

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Souza, PCT, Alessandri, R, Barnoud, J, Thallmair, S, Faustino, I, Grünewald, F, Patmanidis, I, Abdizadeh, H, Bruininks, BMH, Wassenaar, TA, Kroon, PC, Melcr, J, Nieto, V, Corradi, V, Khan, HM, Domański, J, Javanainen, M, Martinez-Seara, H, Reuter, N, Best, RB, Vattulainen, I, Monticelli, L, Periole, X, Tieleman, DP, de Vries, AH & Marrink, SJ 2021, 'Martini 3: a general purpose force field for coarse-grained molecular dynamics', Nature Methods, vol. 18, no. 4, pp. 382-388. https://doi.org/10.1038/s41592-021-01098-3

TY - JOUR

T1 - Martini 3

T2 - a general purpose force field for coarse-grained molecular dynamics

AU - Souza, Paulo C.T.

AU - Alessandri, Riccardo

AU - Barnoud, Jonathan

AU - Thallmair, Sebastian

AU - Faustino, Ignacio

AU - Grünewald, Fabian

AU - Patmanidis, Ilias

AU - Abdizadeh, Haleh

AU - Bruininks, Bart M.H.

AU - Wassenaar, Tsjerk A.

AU - Kroon, Peter C.

AU - Melcr, Josef

AU - Nieto, Vincent

AU - Corradi, Valentina

AU - Khan, Hanif M.

AU - Domański, Jan

AU - Javanainen, Matti

AU - Martinez-Seara, Hector

AU - Reuter, Nathalie

AU - Best, Robert B.

AU - Vattulainen, Ilpo

AU - Monticelli, Luca

AU - Periole, Xavier

AU - Tieleman, D. Peter

AU - de Vries, Alex H.

AU - Marrink, Siewert J.

PY - 2021/4

Y1 - 2021/4

N2 - 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.

AB - 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.

U2 - 10.1038/s41592-021-01098-3

DO - 10.1038/s41592-021-01098-3

M3 - Article

C2 - 33782607

AN - SCOPUS:85103405379

SN - 1548-7091

VL - 18

SP - 382

EP - 388

JO - Nature Methods

JF - Nature Methods

IS - 4

ER -

Martini 3: a general purpose force field for coarse-grained molecular dynamics

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