POPC with 40 and 50 mol-% of cholesterol at 310 K. Slipids force field.

Simulations of a POPC bilayer with varying amounts of cholesterol. This data is employed for the NMRlipids project, see http://nmrlipids.blogspot.fi for more information.

A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) or 50 % (200 molecules) of cholesterol. The Slipids model [1–3] is employed for lipids, and the tip3p model for water.

The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/

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The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), binary run input file for GROMACS v. 4.6–> (.tpr) and the energy output file (.edr) are provided together with the run parameter file (.mdp) employed to run all the simulations.

UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.

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[1] Derivation and Systematic Validation of a Refined 
All-Atom Force Field for Phosphatidylcholine Lipids
Joakim P. M. Jämbeck and Alexander P. Lyubartsev
The Journal of Physical Chemistry B 2012 116 (10), 3164-3179
DOI: 10.1021/jp212503e

[2] An Extension and Further Validation of an All-Atomistic 
Force Field for Biological Membranes
Joakim P. M. Jämbeck and Alexander P. Lyubartsev
Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948
DOI: 10.1021/ct300342n

[3] Another Piece of the Membrane Puzzle: Extending Slipids Further
Joakim P. M. Jämbeck and Alexander P. Lyubartsev
Journal of Chemical Theory and Computation 2013 9 (1), 774-784
DOI: 10.1021/ct300777p