ArticleThe journal of physical chemistry letters2015
A Stochastic Solution to the Unbinned WHAM Equations.
Article in The journal of physical chemistry letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Hydrophobicity in Intrinsically Disordered Protein Force Fields: Implications for Conformational Ensembles and Protein-Protein Interactions.The journal of physical chemistry. B · 2025Article
- FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.Journal of chemical information and modeling · 2025Article
- Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale.The journal of physical chemistry. B · 2025Article
- Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.The journal of physical chemistry. B · 2024Article
- Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations.The Journal of chemical physics · 2023Article
- Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation.Biophysical reviews · 2022Review
- Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins.Nature communications · 2022Article
- Multireference Generalization of the Weighted Thermodynamic Perturbation Method.The journal of physical chemistry. A · 2022Article
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
- Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints.Journal of chemical theory and computation · 2021Article
- Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix.Journal of chemical theory and computation · 2020Article
- Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.Journal of chemical information and modeling · 2019Article
- The UWHAM and SWHAM Software Package.Scientific reports · 2019Article
- Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.Journal of chemical theory and computation · 2019Article
- Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.Journal of chemical information and modeling · 2018Article
- The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations.The journal of physical chemistry. B · 2018Article
- Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.Journal of chemical theory and computation · 2017Article
- Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.Journal of chemical theory and computation · 2017Article
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4 authors.
Funding
Abstract
The weighted histogram analysis method (WHAM) and unbinned versions such as the multistate Bennett acceptance ratio (MBAR) and unbinned WHAM (UWHAM) are widely used to compute free energies and expectations from data generated by independent or coupled parallel simulations. Here we introduce a replica exchange-like algorithm (RE-SWHAM) that can be used to solve the UWHAM equations stochastically. This method is capable of analyzing large data sets generated by hundreds or even thousands of parallel simulations that are too large to be "WHAMMED" using standard methods. We illustrate the method by applying it to obtain free energy weights for each of the 240 states in a simulation of host-guest ligand binding containing ∼3.5 × 10(7) data elements collected from 16 parallel Hamiltonian replica exchange simulations, performed at 15 temperatures. In addition to using much less memory, RE-SWHAM showed a nearly 80-fold improvement in computational time compared with UWHAM.
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