Coarse-grained simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation

<p>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].</p> <p>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).</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>Run parameter files (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 1 ns</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named DOPC_LLLL_CG_CHOLXX_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid in the non-DOPC leaflet</li> <li>CG stands for coarse-grained (All atom data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.</p> <p>[1] <strong>DOI: </strong>10.1021/jp071097f</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00209</p> <p>[3] <strong>DOI:&nbsp;</strong>10.1016/j.softx.2015.06.001</p>