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. DOI:10.1021/ct300646g
Curious? Go here for downloading the Martinize script which now features a beta release of Martini 2.2. Any feedback is appreciated so we can further improve the model.
The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to more realistic length of α-helices and to improved numerical stability for poly-alanine and glycine repeats. The new parameter set is denoted Martini version 2.2.
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