Replica exchange umbrella sampling

Another paper from the Sansom lab showing how protein-protein and protein-lipid PMFs with MARTINI can be efficiently obtained using replica-exchange umbrella sampling:

J. Domanski, G. Hedger, R.B. Best, P.J. Stansfeld, and M.S.P. Sansom. Convergence and sampling in determining free energy landscapes for membrane protein association. J. Phys. Chem. B, Just Accepted. doi:10.1021/acs.jpcb.6b08445

Complexity of the photosynthetic machinery captured by Martini

We proudly present the most recent work of F. J. van Eerden a PhD student in our lab, soon to graduate.

F.J. van Eerden, T. van den Berg, P.W.J.M. Frederix, D.H. de Jong, X. Periole, S.J. Marrink. Molecular dynamics of photosystem II embedded in the thylakoid membrane. JPCB,2016, Accepted Manuscript. doi:10.1021/acs.jpcb.6b06865

toc PSII

Martini metadynamics

Check out this paper, a nice example of how metadynamics can be combined with Martini for efficient sampling of protein-protein binding free energies:

, , and Conformational changes in the epidermal growth factor receptor: role of the transmembrane domain investigated by Coarse-Grained metadynamics free energy calculations.  J. Am. Chem. Soc., Just Accepted. doi:10.1021/jacs.6b05602

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


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