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Calculation of PMF from the WHAM and FEP molecular dynamics simulations: case study of the methane dimer in water
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
2008 (English)In: Chemical Physics Letters, ISSN 0009-2614, Vol. 452, no 1-3, 72-77 p.Article in journal (Refereed) Published
Abstract [en]

Combined use of the weighted histogram analysis method (WHAM) and the free energy perturbation (FEP) method for the calculation of potential of mean force (PMF) from the molecular dynamics simulations is examined for the methane–methane association in TIP3P water with the SCAAS-model spherical boundary. The linear square fit of the informative free-energy profile from the WHAM, but with an uncertain baseline, to the discrete absolute free energies of binding from the FEP calculations yields the PMF with an accurate zero level. Such a procedure may be particularly useful in PMF simulations of biochemical systems when only a short part of the entire reaction pathways is considered.

Place, publisher, year, edition, pages
2008. Vol. 452, no 1-3, 72-77 p.
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-105257DOI: 10.1016/j.cplett.2017.12.017ISI: 000253804500013OAI: oai:DiVA.org:uu-105257DiVA: diva2:220841
Available from: 2009-06-02 Created: 2009-06-02 Last updated: 2010-01-11Bibliographically approved

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