| Title: | Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields |
| Author(s): | Bratek M; Wojcik-Augustyn A; Kania A; Majta J; Murzyn K; |
| Address: | "Department of Computational Biophysics and Bioinformatics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Krakow, Poland" |
| ISSN/ISBN: | 1734-154X (Electronic) 0001-527X (Linking) |
| 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" |
| Keywords: | "Alkanes/*chemistry Diffusion Kinetics Lipid Bilayers/chemistry *Models, Chemical Models, Molecular *Molecular Dynamics Simulation Molecular Structure Phospholipids/chemistry Transition Temperature Viscosity Volatilization;" |
| Notes: | "MedlineBratek, Maciej Wojcik-Augustyn, Anna Kania, Adrian Majta, Jan Murzyn, Krzysztof eng Poland 2020/09/18 Acta Biochim Pol. 2020 Sep 17; 67(3):309-318. doi: 10.18388/abp.2020_5414" |
