Protein side chains

The team of Prof. Vogel has developed a fix to prevent side chains from flipping to the wrong side of beta strands. Soon to be implemented in martinize. For details, see:

F.A. Herzog, L. Braun, I. Schoen, V. Vogel. Improved side chain dynamics in Martini simulations of protein-lipid interfaces. JCTC, online. doi:10.1021/acs.jctc.6b00122

Curvature

A nice study by Wang and Deserno show that the pivotal plane in a Martini DMPC bilayer is located closer to the bilayer center in comparison to an atomistic bilayer. This has important consequences for the interpretation of the effect of curvature on membrane properties. For details, please consult the full paper:

X. Wang, M. Deserno. Determining the tilt modulus by simulating membrane buckles. JPCB, online. doi: 10.1021/acs.jpcb.6b02016

Supercomplex formation

Curious to see what a crowded membrane really looks like? Check out Clement's masterpiece:

C. Arnarez, S.J. Marrink, X. Periole. Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chem. Sci., 2016, online. doi: 10.1039/C5SC04664E

New Perspective

Computational Microscopy

 

We published a perspective on computational modeling (computational 'microscopy') of cell membranes in the imaging series of the Journal of Cell Science:

H.I. Ingólfsson, C. Arnarez, X. Periole, S.J. Marrink. Computational 'microscopy' of cellular membranes.

J. Cell Science, 2016, 

Martini sterols

Keep your membranes fluid: New parameters for cholesterol, ergosterol, and hopanoids

M.N. Melo, H.I. Ingólfsson, S.J. Marrink. Parameters for Martini sterols and hopanoids based on a virtual-site description. JCP, 143, 243152 (2015); http://dx.doi.org/10.1063/1.4937783

Martini straight

Boost your performance using straight cutoffs and GPUs!

D.H. de Jong, S. Baoukina, H.I. Ingólfsson, S.J. Marrink. Martini straight: boosting performance using a shorter cutoff and GPUs. Comp. Phys. Comm., 2015, in press. doi:10.1016/j.cpc.2015.09.014

See the paper for details. Here you can find the required input parameter files to benefit from the increased speed options.