Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields

Maciej Bratek; Anna Wójcik-Augustyn; Adrian Kania; Jan Majta; Krzysztof Murzyn

doi:10.18388/abp.2020_5414

Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields

Maciej Bratek Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
Anna Wójcik-Augustyn Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland https://orcid.org/0000-0002-3053-093X
Adrian Kania Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
Jan Majta Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland https://orcid.org/0000-0001-9042-754X
Krzysztof Murzyn Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland

DOI: https://doi.org/10.18388/abp.2020_5414

Abstract

For over 20 years, the OPLS-All Atom (OPLS-AA) force field has been efficiently used in molecular modelling studies of proteins, carbohydrates and nucleic acids. OPLS-AA is successfully applied in computer modelling of many organic compounds, including decane and shorter alkanes, but it fails when employed for longer linear alkanes, whose chemical structure corresponds to hydrocarbon tails in phospholipids constituting cellular membranes. There have been several attempts to address this problem. In this work, we compare the ability to reproduce various condensed phase properties by six distinct sets of force field parameters which can be assigned to phospholipid hydrocarbon chains. In this comparison, we include three alternative sets of the OPLS-AA force field, as well as the commonly used CHARMM C36, Slipids, and Berger lipids’ parameters.

pdf
html

Published

2020-09-17

Issue

Vol. 67 No. 3 (2020)

Section

Articles

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Acta Biochimica Polonica is an open access quarterly and publishes four issues a year. All contents are distributed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license. Everybody may use the content following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made, ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. There are no additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.