Coarse-grained simulations of cholesterol in symmetric lipid bilayers with restraints on cholesterol positions

<p>Membranes consisting of 520 phospholipids varying levels of chain unsaturation together with 56 (10 mol%) cholesterol molecules were simulated at 298 K. The phospholipids had either 2 (DLiPC) or 4 (DAPC) double bonds in both of their chains. The Martini force field [1] was used and the membranes were generated using insane [2]. In the simulations, a flat-bottom potential was applied to the cholesterol molecules to either prevent them from partitioning to the membrane core, or from performing complete flip&ndash;flops.</p> <p>The simulations were run for 10 microsecond 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) written every 100 ps</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named LLLL_CG_CHOLXX_RR_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid</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>RR is the width of the flat-bottom potential</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. Moreover, md_RR.mdp is common for both lipid types yet activates a different flat-bottom potential based on RR.</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>