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

Martini in Science

Publication featuring the Martini force field in Science:

"Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins"

Pinot et al.,  Science 2014, 345:693-697

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