Martini DNA beta

A beta version of Martini parameters for both single-stranded and double-stranded DNA are available for testing.

The parameters are still under development and currently we recommend testing them in sytems that contain either stable double-stranded DNAs or short single-stranded DNAs.

Read more: Martini DNA beta


adressGood news for multiscalers: Adaptive resolution simulation with MARTINI

J. Zavadlav, M. N. Melo, S.J. Marrink, M. Praprotnik.
Adaptive resolution simulation of an atomistic protein in MARTINI water.
J. Chem. Phys., 140:054114, 2014. open access

Going backward

backwardNew tool for fast backmapping

T.A. Wassenaar, K. Pluhackova, R. Böckmann, S.J. Marrink, D.P. Tieleman.
Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models.
JCTC, 10:676-690, 2014.

For details, read the paper, and/or try out the tool yourself

Coarse grain protein-protein interactions

Review online: "Coarse grain modelling of protein–protein interactions"

M. Baaden, S.J. Marrink. Curr. Opin. Struct. Biol., 23:878:886, 2013. open access

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!


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