title: Atomistic 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 130 molecules, whereas the other leaflet consisted of either 125 DLiPC with 2 double bonds in both chains, 120 DAPC with 4 double bonds in both chains, or 115 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. All systems contained 28 molecules (10 mol%) of cholesterol. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2]. The simulations were run for 1 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file. 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) A common run parameter file (mdp) A run input file (tpr) Trajectory file (xtc) written every 100 ps Energy file (edr) Log file (log) Final structure file (gro) Continue point file (cpt) The files are named DOPC_LLLL_AA_CHOLXX_TTT.FFF, where LLLL is the type of phospholipid paired with DOPC AA stands for all atom (Coarse-grained 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) [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/acs.jctc.5b00935 [3] DOI: 10.1016/j.softx.2015.06.001