Less fuzzy lipids

lipid phase diagrams

A recent study by Carpenter, Lopez and coworkers nicely characterized the phase behavior of Martini DPPC/DOPC/cholesterol ternary mixtures. General Martini parameters correctly captured a large fraction of the phase diagram, but parameters optimized against CHARMM DOPC and DPPC simulations could better capture some of the details, especially close to the critical point.

The new lipid parameters specifically tuned to CHARMM DOPC and DPPC can be found here and in the Martini lipid parameter list: DPPC and DOPC.

For details see JCTC 2018, DOI:10.1021/acs.jctc.8b00496.

Protein-Lipid Interactions


In collaboration with the Tieleman group we published another comprehensive review, focussing on the diversity of protein-lipid interactions. More than 800 references, including many Martini-based studies. sincere apologies if your paper was not included.

V. Corradi, B.I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S.Y. Noskov, S.J. Marrink, D.P. Tieleman. "Emerging Diversity in Lipid–Protein Interactions", Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00451

Complex Membranes

TOC Figure

Together with several co-authors, we wrote a comprehensive review (>700 references) on computer simulations of cell membranes. In this field, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

S.J.Marrink, V. Corradi, P.C.T. Souza, H.I. Ingolfsson, D.P. Tieleman, M.S.P. Sansom. "Computational Modeling of Realistic Cell Membranes". Chem. Review, 2019. DOI:10.1021/acs.chemrev.8b00460

Getting your membranes curved

Boyd and May have deleloped a new tool called BUMPy. The tool allows you to create curved lipid bilayers, combining flexibility of shape, force field, model resolution, and bilayer composition. The tool is avialable online. For details, including many Martini based applications, check the paper: Boyd & May, JCTC, in press, DOI:10.1021/acs.jctc.8b00765

A polarizable MARTINI model for monovalent ions in aqueous solution

FigureIons are known to be tricky when it comes to molecular dynamics. A new polarizable model has been proposed which should have improved behaviour for highly charged models such as DNA and polyelectrolytes. The authors recommend its usage in combination with the refPol forcefield for Martini for best behaviour.

J. Michalowsky, J. Zeman, C. Holm, J. Smiatek, J. Chem. Phys. 149, 163319 (2018); https://doi.org/10.1063/1.5028354

Martini 3 open-beta release

martini cocktailWe gladly announce the release of the open beta version of MARTINI 3. This first glance of the new MARTINI includes all the necessary files to perform CG simulations of phospholipid bilayers and proteins. In the near future, new models for other molecules will also be included in this open beta. So, continue visiting our website to be updated with the news. The main goal of this release is to get feedback from the scientific community. Reporting problems in our forum will help us in the improvement of the force field, which also increase the chances of your favorite system be properly working in the near future. Good feedback is also welcome for the sake of the developers. Be aware, the parametrization is still on-the-fly, which means that the CG models used (from the interaction between beads to the bonded parameters) can/will change until the release and publication of the definitive version.

You can find the open-beta input parameters here.