What question did this study set out to answer?

Introduce and evaluate g_wham, a free implementation of the Weighted Histogram Analysis Method designed to calculate potentials of mean force with robust error and autocorrelation estimation.

November 16, 2010Journal of Chemical Theory and ComputationOpen Access

gwham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

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Authors

JHJochen S. HubCenter for Theoretical Physics BGBert L. de GrootTissue Dynamics (Israel)DSDavid van der SpoelUppsala University

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Implication

Computational study demonstrates robust error estimation via bootstrapping in umbrella sampling simulations, highlighting reduced bias from autocorrelation in inhomogeneous systems.

Key Points

Introduce and evaluate g_wham, a free implementation of the Weighted Histogram Analysis Method designed to calculate potentials of mean force with robust error and autocorrelation estimation.
Implemented three bootstrapping protocols: generating new trajectories from umbrella histograms, bootstrapping complete histograms, and Bayesian bootstrapping using random weights.
Incorporated autocorrelation time calculations into the algorithm to address sampling bias without requiring independent data points for histogram-level bootstrapping.
Bootstrapping generated trajectories yielded accurate error estimates under sufficient sampling, whereas bootstrapping complete histograms prevented error underestimation in the presence of long autocorrelations.
Incorporating autocorrelation times into the method reduced limited sampling bias when computing periodic potentials of mean force in inhomogeneous environments, including lipid membranes and protein channels.

Cite This Study

Hub et al. (2010) studied this question.

synapsesocial.com/papers/69d846e68c03fbaff8beea08 https://doi.org/10.1021/ct100494z

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Implication

Computational study demonstrates robust error estimation via bootstrapping in umbrella sampling simulations, highlighting reduced bias from autocorrelation in inhomogeneous systems.

gwham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

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Implication

Key Points

Cite This Study

gwham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Discussion

Member takes

Implication

Key Points

Cite This Study

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