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  On the convergence of multi-scale free energy simulations

König, G., Brooks, B. R., Thiel, W., & York, D. M. (2018). On the convergence of multi-scale free energy simulations. Molecular Simulation, 44(13-14), 1062-1081. doi:10.1080/08927022.2018.1475741.

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 Creators:
König, Gerhard1, 2, 3, Author              
Brooks, Bernard R.3, Author
Thiel, Walter1, Author              
York, Darrin M.2, Author
Affiliations:
1Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              
2Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, US, ou_persistent22              
3Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA, ou_persistent22              

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Free keywords: Free energy protocol design; multi-scale simulations; convergence properties
 Abstract: In this work, we employ simple model systems to evaluate the relative performance of two of the most important free energy methods: The Zwanzig equation (also known as ‘Free energy perturbation’) and Bennett’s acceptance ratio method (BAR). Although our examples should be transferable to other kinds of free energy simulations, we focus on applications of multi-scale free energy simulations. Such calculations are especially complex, since they connect two different levels of theory with very different requirements in terms of speed, accuracy, sampling and parallelisability. We try to reconcile all those different factors by developing some simple criteria to guide the early stages of the development of a free energy protocol. This is accomplished by quantifying how many λ intermediate steps and how many potential energy evaluations are necessary in order to reach a certain level of convergence.

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Language(s): eng - English
 Dates: 2018-04-112018-05-042018-05-302018-07
 Publication Status: Published in print
 Pages: 20
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1080/08927022.2018.1475741
 Degree: -

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Title: Molecular Simulation
  Other : Mol. Simul.
Source Genre: Journal
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Publ. Info: London, UK : Taylor & Francis Ltd.
Pages: - Volume / Issue: 44 (13-14) Sequence Number: - Start / End Page: 1062 - 1081 Identifier: ISSN: 0892-7022
CoNE: https://pure.mpg.de/cone/journals/resource/954925557477