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MARTINI model development


The use of coarse-grained (CG) models in a variety of simulation techniques has proven to be a powerful tool to probe the spatial and temporal evolution of systems on the microscale, beyond what is feasible with traditional all-atom models.

The MD group is host of the popular MARTINI model, a versatile CG force field for biomolecular simulations. The overall aim of our coarse-graining approach is to provide a simple model that is computationally fast and easy to use, yet flexible enough to be applicable to a large range of systems. Example input files for many systems can be downloaded from http://cgmartini.nl. In collaboration with the group of Peter Tieleman at Univ. of Calgary, we continuously work on systematically improving and further extending of the force field.

[1] H.I. Ingólfsson, C.A. Lopez, J.J. Uusitalo, D.H. de Jong, S. Gopal, X. Periole, S.J. Marrink. The power of coarse-graining in biomolecular simulations. WIREs Comput. Mol. Sci., 4:225–248, 2014
[2] S.J. Marrink, D.P. Tieleman. Perspective on the Martini model. Chem. Soc. Rev., 42:6801-6822, 2013.
[3] D.H. de Jong, G. Singh, W.F.D. Bennett, C. Arnarez, T.A. Wassenaar, L.V. Schäfer, X. Periole, D.P. Tieleman, S.J. Marrink. Improved parameters for the Martini coarse-grained protein force field, JCTC, 9:687–697, 2013
[4] S.O. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink. Polarizable water model for the coarse-grained Martini force field. PLoS Comp. Biol, 6:e1000810, 2010.
[5] C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink. The Martini coarse grained force field: extension to carbohydrates. JCTC, 5:3195-3210, 2009.
[6] L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson, D.P. Tieleman, S.J. Marrink. The MARTINI coarse grained forcefield: extension to proteins. JCTC, 4:819-834, 2008.
[7] S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. The MARTINI forcefield: coarse grained model for biomolecular simulations. JPC-B, 111:7812-7824, 2007.
[8] S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. JPC-B, 108:750-760, 2004.

Martini mapping examples of selected molecules. (A) Standard water particle representing four water molecules. (B) Polarizable water molecule with embedded charges. (C) Phospholipid. (D) Polysaccharide fragment. (E) Peptide. (F) DNA fragment. (G) Polystyrene fragment. (H) Fullerene molecule. Martini CG beads are shown as cyan transparent beads overlaying the atomistic structure.
Martini mapping examples of selected molecules. (A) Standard water particle representing four water molecules. (B) Polarizable water molecule with embedded charges. (C) Phospholipid. (D) Polysaccharide fragment. (E) Peptide. (F) DNA fragment. (G) Polystyrene fragment. (H) Fullerene molecule. Martini CG beads are shown as cyan transparent beads overlaying the atomistic structure.
Last modified:24 June 2015 11.33 p.m.