Another fruitful Martini Workshop
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- Last Updated: Monday, 18 September 2017 10:39
Cherish this picture, for it will contain some nobel price winners in the future!
Sticky sugars
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- Last Updated: Monday, 18 September 2017 10:39
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: Monday, 18 September 2017 10:39
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: Monday, 18 September 2017 10:39
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: Monday, 18 September 2017 10:39
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, 18 September 2017 10:39
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