Power of coarse-graining

Review online: "The power of coarse-graining in biomolecular simulations"

H.I. Ingólfsson, C.A. Lopez, J.J. Uusitalo, D.H. de Jong, S. Gopal, X. Periole, S.J. Marrink.  WIREs Comput. Mol. Sci., in press, 2013. DOI:10.1002/wcms.1169. open access

Website updated

There was a major update on the cgmartini.nl website on August 22nd. Due to the update and a move to a new server, a handful of forum posts between August 20-22 were lost. We are very sorry for the inconvenience.

Physisorption

A Martini model to simulate physisorption of organic molecules on graphite is now available.

Physisorption
 
 
 
Cristian Gobbo, Isabelle Beurroies, David de Ridder, Rienk Eelkema, Siewert J Marrink, Steven De Feyter, Jan H van Esch, Alex H de Vries. MARTINI Model for Physisorption of Organic Molecules on Graphite. J. Phys. Chem. C, 117:15623–15631, 2013.
 
See Gobbo et al. for details.

 

New tools

New tools available: BACKWARD, a python script for fast resolution transformation, INSANE, another python script to build multi-component membranes from scratch, and ANGLEPOT, a package containing a customized version of Gromacs with special angle potentials for increased numerical stability of CG simulations.

New on the Martini pages

Recently, we have added a few new features to the Martini-website. First, there is the Martini-flowchart: if you want to start a new project using the Martini force field but have now idea where to start, this flowchart will get you started step-by-step. Second, we recently started writing a group weblog. Different* group-member will post on a regular* basis what comes to mind related* to the work in the lab. *These terms have to be taken with a grain of salt.

Martini perspective

A review of the Martini force field has appeared, with an overview of one decade of Martini applications, discussion of its limitations, and an outlook on future developments:
S.J. Marrink & D.P. Tieleman, "Perspective on the Martini model",  Chem. Soc. Rev., 42:6801-6822, 2013. Open access