ArticleJournal of chemical theory and computation2014
Theory of Adaptive Optimization for Umbrella Sampling.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking.Journal of chemical theory and computation · 2023Article
- "Dividing and Conquering" and "Caching" in Molecular Modeling.International journal of molecular sciences · 2021Review
- Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4.ACS central science · 2018Article
- A generalized linear response framework for expanded ensemble and replica exchange simulations.The Journal of chemical physics · 2018Article
- Insight into resistance mechanisms of AZD4547 and E3810 to FGFR1 gatekeeper mutation via theoretical study.Drug design, development and therapy · 2017Article
- Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.Journal of computational chemistry · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We present a theory of adaptive optimization for umbrella sampling. With the analytical bias force constant obtained from the constrained thermodynamic length along the reaction coordinate, the windows are distributed to optimize the overlap between neighbors. Combining with the replica exchange method, we propose a method of adaptive window exchange umbrella sampling. The efficiency gain in sampling by the present method originates from the optimal window distribution, in which windows are concentrated to the region where the free energy is steep, as well as consequently improved random walk.
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Registered trials
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