The DAFT approach to membrane protein assembly

Setting up and running many association simulation is now easier than ever. Check out the new tool here and find the paper here.

DAFT TOC

T.A. Wassenaar, K. Pluhackova, A. Moussatova, D. Sengupta, S.J. Marrink, D.P. Tieleman, R.A. Böckmann. High-throughput simulations of dimer and trimer assembly of membrane proteins. The DAFT approach. JCTC, 11:2278–2291, 2015. DOI: 10.1021/ct5010092 abstract

Announcing the 2015 Martini Coarse-Graining Workshop

Are you impressed by the interesting science done by using the Martini coarse-grained model, and do you want to hear from the developers about the philosophy, back-ground, current, and future developments of Martini? Moreover, do you want to practice coarse-graining skills under the guidance of Martini experts? The Martini summerschool is the place for you!

REGISTRATION IS NOW CLOSED - WE ARE FULL!

Read more: Announcing the 2015 Martini Coarse-Graining Workshop

Thylakoid membrane

The thylakoid membrane of spinach

F.J. van Eerden, D.H. de Jong, A.H. de Vries, T. A. Wassenaar, S.J. Marrink. Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. BBA-Biomembranes, 1848:1319–1330, 2015. DOI:10.1016/j.bbamem.2015.02.025

Interested in creating your own thylakoids? Get the starterkit!

PhD Position available

There is a PhD position available at the MD group on Multiscale Modeling of Self-Assembled Molecular Nanotubes. For details see the announcement.

Dry Martini

The Dry Martini paper is outdry-martini

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, a coarse-grained force field for lipid membrane simulations with implicit solvent. JCTC, 11:260–275, 2015. abstract

Try out yourself? Download parameters here.

Plasma membrane

plasma membrane TOCPlasma membrane model composed of 60+ lipid types

H.I. Ingólfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C.A. López, T.A. Wassenaar, X. Periole, A.H. De Vries, D.P. Tieleman, S.J. Marrink. Lipid organization of the plasma membrane. JACS, 136:14554-14559, 2014. doi: 10.1021/ja507832e open access

Example membranes and parameter files are provided here