Dry Martini for lipids

Try out the next flavor of the Martini force field for lipids: Dry Martini. Still without olives.

In this version of Martini, water beads were completely removed from our simulation boxes. We adapted the interactions between beads by slightly tweaking the interaction levels and tuning some bonded parameter to reproduce the properties observed with the standard Martini force field. The new force field developed has been shown to nicely reproduce bilayer properties for a large variety of lipids.

Dry Martini is so far available only for lipids. A couple of small membrane proteins have been shown to perform equivalently compared to the regular Martini model; adaptation for proteins in (dry) solution is still in progress.

Curious? Excited? Download the parameter files and run your first Martini simulations without aqueous solvent!

Dry_Martini_v2.1

Wanna read more? Check this out:
C. Arnarez, J.J. Uusitalo, M.F. Masman, H.I. Ingólfsson, D.H. de Jong, M.N. Melo, X. Periole, A.H. de Vries, S.J. Marrink. Dry Martini: coarse grained implicit water force field for (bio)molecular simulations, JCTC, 11:260–275, 2015. (doi: 10.1021/ct500477k)

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.