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The accelerated weight histogram method for alchemical free energy calculations
ERCO Pharma AB, S-11439 Stockholm, Sweden..
KTH, Skolan för teknikvetenskap (SCI), Fysik, Kondenserade materiens teori.ORCID-id: 0000-0002-9881-7857
KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0002-7498-7763
2021 (engelsk)Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, nr 20, artikkel-id 204103Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.

sted, utgiver, år, opplag, sider
AIP Publishing , 2021. Vol. 154, nr 20, artikkel-id 204103
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URN: urn:nbn:se:kth:diva-302010DOI: 10.1063/5.0044352ISI: 000692823300002PubMedID: 34241154Scopus ID: 2-s2.0-85106877320OAI: oai:DiVA.org:kth-302010DiVA, id: diva2:1594709
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QC 20210916

Tilgjengelig fra: 2021-09-16 Laget: 2021-09-16 Sist oppdatert: 2022-06-25bibliografisk kontrollert

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Lidmar, JackHess, Berk

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