POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog

2018-05-24T00:23:41Z (GMT) by Javanainen, Matti Kulig, Waldemar

Input parameter files and parts of the resulting trajectories for a POPC bilayer simulation with varying amounts of cholesterol. The systems contain 0, 10, 40, 50 or 60 mol-% cholesterol and a total of 128 lipids (POPC+cholesterol). The force field is an extension to the OPLS-based force field by the same authors [1]. All simulations are conducted by Waldemar Kulig and the simulations with 0, 10 and 40 mol-% cholesterol have earlier been discussed in [2].

––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––

Files:

md_cholXX.tpr – XX mol-% cholesterol; run input file for Gromacs versions 4.6 and above. 

md_cholXX.xtc – The last 200 ns of a 400 ns long simulation (200 ns discarded from the beginning). XX mol-% cholesterol. Data saved every 100 ps.

––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––

This data is used in the project "Matching lipid force fields with NMR data", see: http://nmrlipids.blogspot.fi and referred to in the blog as 'MacRog'

[1] Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., and Rog, T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration. The Journal of Physical Chemistry B 118, 4571–4581 (2014). DOI: 10.1021/jp5016627

[2] Kulig, W., Jurkiewicz, P., Olzynska, A., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Hof, M., Vattulainen, I. and Jungwirth, P. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. Biochimica et Biophysica Acta (BBA) - Biomembranes 1848, 422–432 (2015). DOI: 10.1016/j.bbamem.2014.10.032

Categories

Keyword(s)

License

CC0