ArticleThe Journal of chemical physics2016
Eigenvector method for umbrella sampling enables error analysis.
Article in The Journal of chemical physics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Altered morphology and diffusivity of water confined in MXenes: Machine learning-accelerated computations combined with experiments.Science advances · 2026Article
- Gaussian Process Regression for Mapping Free EnergyLandscape of MgMolecules (Basel, Switzerland) · 2025Article
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Computing equilibrium free energies through a nonequilibrium quench.The Journal of chemical physics · 2024Article
- Predicting rare events using neural networks and short-trajectory data.Journal of computational physics · 2023Article
- A New Approach for Estimating the Free Energy Differences among Multiple Thermodynamic States in Statistical Simulations.The journal of physical chemistry letters · 2023Article
- Understanding the sources of error in MBAR through asymptotic analysis.The Journal of chemical physics · 2023Article
- Computing transition path theory quantities with trajectory stratification.The Journal of chemical physics · 2022Article
- Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.Journal of chemical theory and computation · 2021Article
- Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding.The journal of physical chemistry. B · 2020Article
- Stratification as a general variance reduction method for Markov chain Monte Carlo.SIAM/ASA journal on uncertainty quantification · 2020Article
- Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Trajectory stratification of stochastic dynamics.SIAM review. Society for Industrial and Applied Mathematics · 2018Article
- Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.Journal of chemical theory and computation · 2017Article
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Authors and funding
4 authors.
Funding
Abstract
Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare states of a model by biasing simulations to windows of coordinate values and then combining the resulting data with physical weighting. Here, we introduce a mathematical framework that casts the step of combining the data as an eigenproblem. The advantage to this approach is that it facilitates error analysis. We discuss how the error scales with the number of windows. Then, we derive a central limit theorem for averages that are obtained from umbrella sampling. The central limit theorem suggests an estimator of the error contributions from individual windows, and we develop a simple and computationally inexpensive procedure for implementing it. We demonstrate this estimator for simulations of the alanine dipeptide and show that it emphasizes low free energy pathways between stable states in comparison to existing approaches for assessing error contributions. Our work suggests the possibility of using the estimator and, more generally, the eigenvector method for umbrella sampling to guide adaptation of the simulation parameters to accelerate convergence.
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Registered trials
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