Skip to ContentSkip to Navigation
ResearchMolecular Dynamics Group

Try out now! Martini 2.2: Improved parameters for the protein force field

24 May 2013

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.

Last modified:12 March 2019 11.57 a.m.

More news

  • 11 July 2019

    Major companies’ annual reports too vague about climate impact

    Many major Dutch companies publish extensive information about climate impact in their annual reports. However, very few companies provide concrete, detailed information about their own CO2 emissions, the impact of climate change on their business...

  • 08 July 2019

    UG permanently closes Yantai project

    The University of Groningen (UG) has permanently closed the project aimed at creating a branch campus in Yantai. Discussions were held with China Agricultural University, the city of Yantai and the Province of Shandong.

  • 03 July 2019

    Cheap train tickets boost public transport use but reduce customer satisfaction

    Offers of cheap single train tickets through retailers such as Kruidvat or Etos have a positive impact on the number of kilometres travelled by rail. This impact is much bigger than that of more general TV, newspaper or magazine advertising. However,...