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Crowds slow you down

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Last Updated: Monday, 21 August 2017 12:23

What happens to the famous Saffman-Delbruck model when your membrane is crowded with proteins ? Read all about it in this exciting new paper from the Vattulainen group, featuring Martini simulations of very crowded membranes:

M. Javanainen, H. Martinez-Seara, R. Metzler, I. Vattulainen, J. Phys. Chem. Lett. 2017, available online

Sticky sugars

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Last Updated: Wednesday, 16 August 2017 15:32

Be aware of the fact that self interactions of large biomolecules in Martini are sometimes too strong and may lead to arteficial aggregation - see for instance the recent work of the group of Sikora on polysaccharides:

P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.P. Heisenberg, M. Sikora. JCTC, in press. DOI: 10.1021/acs.jctc.7b0037410.1021/acs.jctc.7b00374

 Note: with the forthcomng release of Martini 3.0, we aim to resolve this issue !

Supramolecular polymer dynamics

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Last Updated: Tuesday, 15 August 2017 11:35

The group of Pavan has used Martini in combination with well-tempered metadynamics to study the self-healing capacity of bio-inspired supramolecular polymers. Cool !

D. Bochicchio, M. Salvalaglio, G. Pavan. Nature Commun. 8:147 (2017).

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: Wednesday, 05 July 2017 21:25

rna Figure7

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