In memoriam Herman Berendsen

Herman_Berendsen.jpgHerman Berendsen, one of the founding fathers of molecular modeling, passed away last Monday at the respectable age of 85.

We will miss him, but his legacy is large and will last for generations to come.

MARTINI practical guide

If you would like some guidance on how to setup complex MARTINI simulations, the tips and tricks behhind the scene, have a look at this book chapter: Bruininks et al., "A Practical View of the Martini Force Field", Biomolecular Simulations, 105-127, 2019. pdf-reprint.

Pitfalls of MARTINI

As you hopefully would agree, MARTINI can provide you with beautiful simulations that are undoable with all-atom models. However, it is good to always stay aware of the shortcomings of the model. No free lunch ! In a recent paper we discuss some of these shortcomings that result from the building block principle underlying our model (as well as other CG models). We also discuss potential remedies, providing the rationale for the improvements made in the forthcoming Martini 3.0 version. Enjoy !

Alessandri et al., Pitfalls of the MARTINI model. JCTC, in press.

Protein (had)docking with MARTINI

The group of Bonvin has implemented a scoring function for protein-protein docking, based on the Martini force field, in their popular HADDOCK software package. For details, see: Roel-Touris et al., 

Another paper describes the successful HADdocking of protein-DNA complexes using Martini: Honorato et al., Front. Mol. Biosci., 2019 |

Toxins destroy membrane


Martini simulations from the Hummer group show how toxic peptides form big pores in cholesterol containing membranes.

For details, see: Vogele et al., PNAS 2019,


A web server for setting up and running Martini membrane systems has just been launched:

M. Damre, A. Marchetto, A. Giorgetti. MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. Nucleic Acids Research, gkz416, doi:10.1093/nar/gkz416.