Go Martini

Looking for a way to model foldable Martini proteins? Try Go Martini, a clever combination of Martini and Go potentials developed by the group of Theodorakis. Further details on the method can be found in the publication:

A.B. Poma, M. Cieplak, P.E. Theodorakis, JCTC, 13:1366–1374, 2017. DOI:10.1021/acs.jctc.6b00986

Crowds slow you down

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

Another fruitful Martini Workshop

Cherish this picture, for it will contain some nobel price winners in the future!group picture Martiniworkshop 2017

Sticky sugars

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

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

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