ArticleMolecular simulation
Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace.
Article in Molecular simulation. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Endosome rupture enables enteroviruses from the family Picornaviridae to infect cells.Communications biology · 2024Article
- A New Approach for Estimating the Free Energy Differences among Multiple Thermodynamic States in Statistical Simulations.The journal of physical chemistry letters · 2023Article
- Capsid opening enables genome release of iflaviruses.Science advances · 2021Article
- A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.Journal of computational chemistry · 2020Article
- Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly.ACS infectious diseases · 2019Article
- Enterovirus particles expel capsid pentamers to enable genome release.Nature communications · 2019Article
- The UWHAM and SWHAM Software Package.Scientific reports · 2019Article
- Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.Journal of chemical theory and computation · 2017Article
- Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.The Journal of chemical physics · 2016Article
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3 authors.
Funding
Abstract
The weighted histogram analysis method (WHAM) for free energy calculations is a valuable tool to produce free energy differences with the minimal errors. Given multiple simulations, WHAM obtains from the distribution overlaps the optimal statistical estimator of the density of states, from which the free energy differences can be computed. The WHAM equations are often solved by an iterative procedure. In this work, we use a well-known linear algebra algorithm which allows for more rapid convergence to the solution. We find that the computational complexity of the iterative solution to WHAM and the closely-related multiple Bennett acceptance ratio (MBAR) method can be improved by using the method of direct inversion in the iterative subspace. We give examples from a lattice model, a simple liquid and an aqueous protein solution.
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