Title: POPC @ 310K, model by Maciejewski and Rog

Type Dataset Javanainen, Matti (2014): POPC @ 310K, model by Maciejewski and Rog. Zenodo. Dataset. https://zenodo.org/record/13497

Author: Javanainen, Matti (TUT) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

Input parameter file and part of the resulting trajectory for a POPC bilayer simulation. The force field is an extension to the OPLS-based force field by the same authors [1]. The same POPC force field has also been employed in [2].

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'. Note that this upload contains data every 100 ps between 30–110 ns of the simulation, whereas data every 10 ps in the interval 20–100 ns are employed in the results reported in the blog. This should have a diminishing effect on the results.

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Files:

md.tpr – run input file for Gromacs versions 4.6.3 and above

md_100ps.xtc – The last 80 ns of a 110 ns long simulation. Data saved every 100 ps.

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[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.13497

Dates

• Publication date: 2014
• Issued: December 30, 2014

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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