title: Coarse-grained simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation
author: Javanainen, Matti
description: Asymmetric membranes consisting of DOPC, cholesterol, and a lipid with a varying level of unsaturation were simulated at 310 K. The DOPC leaflet consisted of 520 molecules, whereas the other leaflet consisted of either 520 DLiPC with 2 double bonds in both chains, 520 DAPC with 4 double bonds in both chains, or 468 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. Additionally, a symmetric DOPC membrane of the same size (520+520 lipids) was simulated. All systems also contained 112 molecules (10 mol%) of cholesterol. The Martini force field [1] was used and the membranes were generated using insane [2]. The simulations were run for 50 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations). The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data: Topology files (top) and molecular definitions (itp) Index files (ndx) Run parameter files (mdp) A run input file (tpr) Trajectory file (xtc) written every 1 ns Energy file (edr) Log file (log) Final structure file (gro) Continue point file (cpt) The files are named DOPC_LLLL_CG_CHOLXX_TTT.FFF, where LLLL is the type of phospholipid in the non-DOPC leaflet CG stands for coarse-grained (All atom data in a separate upload) CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%) TTT is the temperature FFF is the tile type (see above) Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. [1] DOI: 10.1021/jp071097f [2] DOI: 10.1021/acs.jctc.5b00209 [3] DOI: 10.1016/j.softx.2015.06.001