Lipid membranes

DIY Thylakoid simulation kit

The thylakoid membrane of spinach

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

plasma membrane TOCAn idealized mammalian plasma membrane composed of 63 different lipid types. 

H.I. IngólfssonM.N. MeloF.J. van EerdenC. ArnarezC.A. LópezT.A. WassenaarX. PerioleA.H. De VriesD.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.

plasma_membrane.zip

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

plasma_membrane_small.zip

Glycolipid membranes

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

 

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.

raft.gro
raft.mpd
raft.top

Bolalipid membranes

Systems of pure cyclic and acyclic bolalipid bilayers:

  • 128 cyclic di-dPPC (all trans) at T = 363
  • 126 cyclic di-DPPC (122 trans - 4 loop) at T = 363
  • 128 acyclic di-DPPC (all trans) at T = 323
  • 128 acyclic di-DPPC (112 trans 16 loop) at T = 323
  • 26 cyclic di-DPPC (trans) + 204 DPPC  at T = 323
bola-cyclic-128trans.gro
bola-cyclic-122trans-4loop.gro
bola-cyclic.mdp
bola-cyclic.top
bola-acyclic-128trans.gro
bola-acyclic-112trans-16loop.gro
bola-acyclic.mdp
bola-acyclic.top
bola-cyclic+dppc.gro
bola-cyclic+dppc.mdp
bola-cyclic+dppc.top

Poly-unsaturated lipid/cholesterol bilayer

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

dapc_chol.gro
dapc_chol.mdp
dapc_chol.top

DPPC/cholesterol bilayer

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

dppc_chol.gro
dppc_chol.mdp
dppc_chol.top

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.

triton_dppc.tgz

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.

peroxidized-martini-lipids.zip

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