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

Type Dataset Javanainen, Matti, Kulig, Waldemar (2015): POPC/Cholesterol @ 310K. 0, 10, 40, 50 and 60 mol-% cholesterol. Model by Maciejewski and Rog. Zenodo. Dataset. https://zenodo.org/record/3252052

Authors: Javanainen, Matti (TUT) ; Kulig, Waldemar (TUT) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

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].

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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.

UPDATE: 500 ns long trajectories of 0, 10, 40, and 50 mol% simulatios and the respective cpt files were uploaded.

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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

More information

• DOI: 10.5281/zenodo.3252052

Dates

• Publication date: 2015
• Issued: January 11, 2015

Rights

• https://creativecommons.org/publicdomain/zero/1.0/legalcode Creative Commons Zero v1.0 Universal
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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