54:(O-IX). The beads can be used at normal size (4:1 mapping), S-size (small, 3:1 mapping) or T-size (tiny, 2:1 mapping). The S-particles are mainly used in ring structures whereas the T-particles are currently used in nucleic acids only. Bonded interactions (bonds, angles, dihedrals, and impropers) are derived from atomistic simulations of crystal structures.
155:(β-sheets), are constrained. Martini proteins are often simulated in combination with an elastic network, such as Elnedyn, to maintain the overall structure. However, the use of the elastic network restricts the use of the Martini force field for the study of large conformational changes (e.g. folding). The GōMartini approach introduced by Poma
53:
For the
Martini force field 4 bead categories have been defined: Q (charged), P (polar), N (nonpolar), and C (apolar). These bead types are in turn split in 4 or 5 different levels, giving a total of 20 beadtypes. For the interactions between the beads, 10 different interaction levels are defined
386:
van den
Bogaart, Geert; Meyenberg, Karsten; Risselada, H. Jelger; Amin, Hayder; Willig, Katrin I.; Hubrich, Barbara E.; Dier, Markus; Hell, Stefan W.; GrubmĂĽller, Helmut; Diederichsen, Ulf; Jahn, Reinhard (24 November 2011).
666:
Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A. (8 September 2009). "Combining an
Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition".
41:
of lipids, later (2007) extended to various other molecules. The force field applies a mapping of four heavy atoms to one CG interaction site and is parametrized with the aim of reproducing thermodynamic properties.
66:. The original 2004 and 2007 papers have been cited 1850 and 3400 times, respectively. The force field has been implemented in three major simulation codes: GROningen MAchine for Chemical Simulations (
753:
LĂłpez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; HĂĽnenberger, Philippe H.; Marrink, Siewert J. (2009). "Martini Coarse-Grained Force Field: Extension to
Carbohydrates".
621:
Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier; Larson, Ronald G.; Tieleman, D. Peter; Marrink, Siewert-Jan (1 May 2008). "The MARTINI Coarse-Grained Force Field: Extension to
Proteins".
1003:
Rossi, Giulia; Monticelli, Luca; Puisto, Sakari R.; Vattulainen, Ilpo; Ala-Nissila, Tapio (2011). "Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case".
231:
202:
956:"Coarse-Grained Molecular Dynamics Studies of the Concentration and Size Dependence of Fifth- and Seventh-Generation PAMAM Dendrimers on Pore Formation in DMPC Bilayer"
183:
Parameters for different other molecules, including carbon nanoparticles, ionic liquids, and a number of polymers, are available from the
Martini website.
279:
207:
714:"Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins"
503:
Schäfer, Lars V.; De Jong, D. H.; Holt, A.; Rzepiela, A. J.; De Vries, A. H.; Poolman, B.; Killian, J. A.; Marrink, S. J. (25 January 2011).
62:
The
Martini force field has become one of the most used coarse grained force fields in the field of molecular dynamics simulations for
1120:
923:"Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction"
128:
1038:
Alessandri, Riccardo; Uusitalo, Jaakko J.; de Vries, Alex H.; Havenith, Remco W. A.; Marrink, Siewert J. (2017).
83:
505:"Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes"
327:
Souza, Paulo C. T.; Alessandri, Riccardo; Barnoud, Jonathan; Thallmair, Sebastian; et al. (29 March 2021).
278:
Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H. (1 July 2007).
921:
Vazquez-Salazar, Luis Itza; Selle, Michele; de Vries, Alex H.; Marrink, Siewert J.; T. Souza, Paulo C. (2020).
17:
1040:"Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations"
31:
27:
788:
Uusitalo, Jaakko J.; IngĂłlfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J. (2015).
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louhivuori, Martti; Risselada, H. J.; Van Der
Giessen, E.; Marrink, S. J. (16 November 2010).
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Uusitalo, Jaakko J.; IngĂłlfsson, Helgi I.; Marrink, Siewert J.; Faustino, Ignacio (2017).
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421:
388:
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886:
Monticelli, Luca (2012). "On atomistic and coarse-grained models for C60 fullerene".
360:
329:"Martini 3: a general purpose force field for coarse-grained molecular dynamics"
148:
124:
63:
45:
In 2021, a new version of the force field has been published, dubbed
Martini 3.
344:
854:
152:
116:
38:
806:
789:
730:
713:
446:"Release of content through mechano-sensitive gates in pressurized liposomes"
328:
588:
529:
470:
280:"The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations"
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989:
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Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E. (1 January 2004).
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87:
67:
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295:
247:
175:
Compatible parameters were released for DNA in 2015 and RNA in 2017.
108:
71:
389:"Membrane protein sequestering by ionic protein–lipid interactions"
78:). Notable successes are simulations of the clustering behavior of
197:
131:
with other bilayer properties, and more complex bilayer behavior.
120:
104:
79:
86:(MscL) and the simulation of the domain partitioning of membrane
375:
https://scholar.google.com/citations?hl=nl&user=UalQWxIAAAAJ
75:
712:
Poma, Adolfo; Cieplak, M.; Theodorakis, P. E. (24 Feb 2017).
232:"Coarse Grained Model for Semiquantitative Lipid Simulations"
1086:
1103:
203:
Comparison of software for molecular mechanics modeling
831:"Martini Coarse-Grained Force Field: Extension to RNA"
790:"Martini Coarse-Grained Force Field: Extension to DNA"
564:"The molecular face of lipid rafts in model membranes"
562:
Risselada, H. J.; Marrink, S. J. (11 November 2008).
568:Proceedings of the National Academy of Sciences
933:(21). Royal Society of Chemistry: 7376–7386.
167:Compatible parameters were released in 2009.
8:
103:The initial papers contained parameters for
718:Journal of Chemical Theory and Computation
669:Journal of Chemical Theory and Computation
623:Journal of Chemical Theory and Computation
305:11370/5bdbbb23-2e1a-48a4-8c27-e1b8c28d74d6
257:11370/6f357aca-0e36-4e9f-880c-62a50aff9ccd
30:developed by Marrink and coworkers at the
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208:Comparison of force field implementations
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127:. They semiquantitatively reproduce the
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223:
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147:. Secondary structure elements, like
74:), and Nanoscale Molecular Dynamics (
7:
82:, the simulations of the opening of
960:The Journal of Physical Chemistry B
284:The Journal of Physical Chemistry B
236:The Journal of Physical Chemistry B
70:), GROningen MOlecular Simulation (
34:, initially developed in 2004 for
14:
373:Google Scholar, 14 October 2019,
954:Lee, H.; Larson, R. G. (2008).
28:coarse-grained (CG) force field
143:were introduced by Monticelli
1:
1137:
345:10.1038/s41592-021-01098-3
139:Compatible parameters for
129:phase behavior of bilayers
15:
855:10.1016/j.bpj.2017.05.043
159:removes this limitation.
84:mechanosensitive channels
1121:Force fields (chemistry)
807:10.1021/acs.jctc.5b00286
731:10.1021/acs.jctc.6b00986
589:10.1073/pnas.0807527105
530:10.1073/pnas.1009362108
471:10.1073/pnas.1001316107
32:University of Groningen
888:J. Chem. Theory Comput
794:J. Chem. Theory Comput
755:J. Chem. Theory Comput
509:Proc Natl Acad Sci USA
450:Proc Natl Acad Sci USA
1056:10.1021/jacs.6b11717
16:For other uses, see
1017:2011SMat....7..698R
847:2017BpJ...113..246U
580:2008PNAS..10517367R
574:(45): 17367–17372.
521:2011PNAS..108.1343S
462:2010PNAS..10719856L
456:(46): 19856–19860.
413:10.1038/nature10545
405:2011Natur.479..552V
1025:10.1039/C0SM00481B
940:10.1039/D0GC01823F
119:, a wide range of
36:molecular dynamics
1050:(10): 3697–3705.
972:10.1021/jp802606y
966:(26): 7778–7784.
900:10.1021/ct3000102
767:10.1021/ct900313w
761:(12): 3195–3210.
691:10.1021/ct9002114
645:10.1021/ct700324x
399:(7374): 552–555.
296:10.1021/jp071097f
290:(27): 7812–7824.
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153:beta sheets
125:cholesterol
117:surfactants
80:syntaxin-1A
835:Biophys. J
214:References
39:simulation
677:CiteSeerX
631:CiteSeerX
361:232421378
107:, simple
1115:Category
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353:33782607
314:17569554
187:See also
141:proteins
135:Proteins
88:peptides
49:Overview
1065:5355903
1013:Bibcode
981:2504730
864:5529176
843:Bibcode
599:2579886
576:Bibcode
540:3029762
517:Bibcode
481:2993341
458:Bibcode
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193:GROMACS
109:alkanes
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72:GROMOS
357:S2CID
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179:Other
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26:is a
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310:PMID
151:and
123:and
76:NAMD
1060:PMC
1052:doi
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1021:doi
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409:doi
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300:hdl
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58:Use
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