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BioExcel Webinar #54: Applying the Accelerated Weight Histogram method to alchemical transformations

Authors: Magnus Lundborg; Berk Hess;

BioExcel Webinar #54: Applying the Accelerated Weight Histogram method to alchemical transformations

Abstract

Alchemical transformations are regularly used to compute free energies of solvation, binding and mutation. The end states of interest are connected by a path using a coupling parameter lambda. The standard procedure is to run multiple simulations, each at a fixed value of lambda, and use Bennett’s acceptance ratio to obtain the free energy difference. In this webinar we present how the Accelerated Weight histogram method can be used for such calculations. In this approach lambda is varied dynamically in a single simulation, and the free energy difference can be obtained directly. This has been implemented in the GROMACS 2021 release and provides a simple and flexible way to compute alchemical free energies and can be trivially parallelized using multiple walkers (copies of the system).

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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