Coarse Grain Forcefield for Biomolecules

Enhanced sampling with iMapD

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Last Updated: Thursday, 22 June 2017 07:32

Check out this new method for fast sampling by Hummer and coworkers. They introduce "iMapD", a method to enhance the exploration in an MD simulation with no prior knowledge of a suitable collective variable. The method was applied to simulations of the Mga2 dimer in Martini and enabled, for the first time, observation of an unbiased dissociation path.

Chiavazzo, Covino, et al., PNAS, online: http://www.pnas.org/content/early/2017/06/19/1621481114.full

RNA extension in Martini

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Last Updated: Tuesday, 20 June 2017 12:04

Now we can also simulate RNA systems with Martini. Check out our publication in Biophysical Journal. Single strand and double strand RNA molecules can now be simulated together with other biomolecules. You can download the parameters here.

 J.J. Uusitalo, H.I. Ingólfsson, S.J. Marrink, I. Faustino. MARTINI coarse-grained force field: extension to RNA. Biophys. J., online, 2017. DOI: http://dx.doi.org/10.1016/j.bpj.2017.05.043

Martinizing VISM

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Last Updated: Monday, 19 June 2017 09:25

Check out this cool paper,  pushing the Variational Implicit Solvent Method (VISM) to larger scale applications by combining it with solute Hamiltonians adapted from the MARTINI framework: 
C.G. Ricci, B. Li, L.T. Cheng, J. Dzubiella, J.A. McCammon. JPCB, 2017. online

MD simulations reveal chaos in electron transport

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Last Updated: Thursday, 11 May 2017 12:51

Using Martini, we were able to simulate the spontaneous binding and unbinding of electron carriers to photosystem II, one of the key protein complexes in photosynthesis. For more details, please see the full paper:

F.J. van Eerden, M.N. Melo, P.W.J.M. Frederix, X. Periole, S.J. Marrink. Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Commun. 8:15214, 2017. http://rdcu.be/rU3i

or check out the various press releases (including a cool movie):

Announcing the 2017 Martini Coarse-Graining Workshop

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Last Updated: Wednesday, 10 May 2017 18:50

Are you impressed by the interesting science done by using the Martini coarse-grained model, and do you want to hear from the developers about the philosophy, background, current, and future developments of Martini? Moreover, do you want to practice coarse-graining skills under the guidance of Martini experts? The Martini summerschool is the place for you!

Registration closed

Read more: Announcing the 2017 Martini Coarse-Graining Workshop