Lipid membranes

Epithelial plasma membrane

Thanks to Stephen Fairweather, and the excellent work of O’Mara and coworkers, we are happy to share newly parameterized Martini models of lipids such as plasmalogens, hyrdoxylated sphingholipids, and Forssman lipids. For more information, check out the publication: https://doi.org/10.1063/5.0040887

You can download the topologies and other data from here!

Brain plasma membrane

An idealized brain plasma membrane composed of 58 different lipid types.

For simulation files and parameters, see bbs.llnl.gov/neuronal-membrane-data.html

  • H.I. Ingólfsson, T.S. Carpenter, H. Bhatia, P.T. Bremer, S.J. Marrink, F.C. Lightstone. Computational Lipidomics of the Neuronal Plasma Membrane. Biophys. J. 113:2271–2280, 2017. open access

DIY Thylakoid simulation kit

Everything you need in order to simulate your own thylakoid membrane.

This package contains both coarse grained and fine grained parameter files for the simulation of the thylakoid membranes of cyanobacteria (Thermosynechococcus vulcanus) and plants (spinach, Spinacia oleracea)

  • 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

Plasma membrane

An idealized mammalian plasma membrane composed of 63 different 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, and S.J. Marrink. Lipid organization of the plasma membrane. JACS, online. DOI: 10.1021/ja507832e

Force field parameters are provided for all the lipids used as well as setup and coordinate files for the large plasma membrane simulation (~20.000 lipids) at 0, 20 and 40 microseconds.

And for a smaller (~6.600 lipids) simulation after 10 microseconds.

Glycolipid membranes

Parameter files for various membranes composed of glycolipids (MGDG, DGDG, SQDG, PI, PIP2, GCER, GM1)

Bi-lamellar DOPE system

Non-equilibrated, expected to form an inverted hexagonal phase at T > 330K. System composition: lipids 1024, water 800.

Model raft bilayer

Equilibrated at T=295K, zero surface tension. System composition: DPPC 828, Di-C18:2-PC 540, cholesterol 576 (0.42:0.28:0.3 ratio), water 12600.

Bolalipid membranes

Systems of pure cyclic and acyclic bolalipid bilayers:

Poly-unsaturated lipid/cholesterol bilayer

Equilibrated at T=298K, zero surface tension. System composition: DAPC 38, cholesterol 4 (0.1 mole fraction), water 142.

DPPC/cholesterol bilayer

Equilibrated at T=300K, zero surface tension. System composition: DPPC 38, cholesterol 16 (0.3 mole fraction), water 350.

DOPC and POPE membranes

Equilibrated at T=300K, zero surface tension. System size: lipids 128, water 1500. Warning these bilayers were constructed using self-assembly and can therefore be slightly asymmetrical, for guaranteed symmetrical bilayers we advise using a bilayer building tool, such as insane.

DPPC bilayer

Equilibrated at T=325K, zero surface tension. System size: lipids 128, water 2000.

Triton TX-100 in a DPPC bilayer

(provided by Antonio De Nicola, www.smms.unisa.it)

Parameter file for Triton TX-100, a .gro and .top files of a DPPC bilayer with TX-100 inserted and a simulation parameter file.

The corresponding article can be cited as:

  • MARTINI Coarse‑Grained Model of Triton TX‑100 in Pure DPPC Monolayer and Bilayer Interfaces. Antonio Pizzirusso, Antonio De Nicola, and Giuseppe Milano. The Journal of Physical Chemistry B, Just Accepted Manuscript. DOI:http://dx.doi.org/10.1021/acs.jpcb.6b00646

Peroxidized lipids

(provided by Fabrice Thalmann, http://www.ics-cnrs.unistra.fr/Mcube)

Parameter file for peroxidized POPC and DOPC and a 512 (256 per leaflet) small lipid bilayer and a 8192 (4096 per leaflet) large lipid bilayer.

The corresponding article can be cited as

Peroxidised phospholipid bilayers: insight from coarse-grained molecular dynamics simulations. Y. Guo, V.A. Baulin, F. Thalmann. Soft Matter, 12, 263–271. 2015. doi.org/10.1039/C5SM01350J