Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core

<p>Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].</p> <p>For simulations without a restrained cholesterol, see the other upload at DOI:</p> <p>The simulations were run for 2 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>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 100 ps</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 LLLL_AA_CHOLXX_CORE_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid</li> <li>AA stands for all atom (Coarse-grained 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/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p>[3] <strong>DOI:&nbsp;</strong>10.1016/j.softx.2015.06.001</p>