POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field.

Simulations of a POPC bilayer with varying amounts<br> of cholesterol. This data is employed for the NMRlipids<br> project, see <em>http://nmrlipids.blogspot.fi</em> for more information. A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Slipids model [1–3] is employed for lipids,<br> and the tip3p model for water. The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/ –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index file (.ndx),<br> binary run input file for GROMACS v. 4.6–&gt; (.tpr) and the<br> energy output file (.edr) are provided together with the run<br> parameter file (.mdp) employed to run all the simulations. UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files. –––––––––––––––––––––––––––––––––––––––––––––––––––––– [1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e [2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n [3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p