title: POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Slipids with default Amber ions
author: Javanainen, Matti
description: Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Slipids model [1–3] is employed for lipids, tip3p model for water, and the default amber ion parameters (type C0) for CaCl_2. The Slipids force field parameters are available at http://www.fos.su.se/~sasha/SLipids/ . –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 4.6->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided. –––––––––––––––––––––––––––––––––––––––––––––––––––––– [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  