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A new AMBER-compatible force field parameter set for alkanes
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
2014 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 20, no 3, 2143- p.Article in journal (Refereed) Published
Abstract [en]

We present a new force field parameter set for simulating alkanes. Its functional form and parameters are chosen to make it directly compatible with the AMBER94/99/12 family of force fields implemented in the available software. The proposed parameterization enables universal description of both the conformational and thermodynamic properties of linear, branched, and cyclic alkanes. Such unification is achieved by using two essential principles: (1) reduction of the Lennard-Jones radius for all sp3 carbons to 1.75 angstrom; (2) separate optimization of Lennard-Jones well depths for carbons with different degree of substitution. The new parameter set may prove to be optimal for description of alkyl residues in a broad range of biomolecules, from amino acids to lipids with their extended linear tails.

Place, publisher, year, edition, pages
2014. Vol. 20, no 3, 2143- p.
Keyword [en]
AMBER, Force field, Hydrocarbons, Molecular dynamics, OPLS
National Category
Biochemistry and Molecular Biology Chemical Sciences Biophysics Computer Science
Identifiers
URN: urn:nbn:se:su:diva-102467DOI: 10.1007/s00894-014-2143-6ISI: 000332180100037OAI: oai:DiVA.org:su-102467DiVA: diva2:710763
Funder
Swedish Research Council, 621-2010-5005
Note

AuthorCount:3;

Available from: 2014-04-08 Created: 2014-04-07 Last updated: 2017-12-05Bibliographically approved

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