ArticleJournal of chemical theory and computation2025
Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation.Journal of chemical theory and computation · 2026Article
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- On Free Energy Calculations in Drug Discovery.Accounts of chemical research · 2025Article
- Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway.The journal of physical chemistry. B · 2025Article
- Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding.Journal of chemical information and modeling · 2025Article
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Authors and funding
4 authors.
Funding
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Abstract
While nowadays approaches for equilibrium free energy estimation are well established, nonequilibrium simulations represent both an appealing computational opportunity and a challenge. This kind of simulations allows for a trivially parallel scheme, but at the same time the significant amount of irreversible work often generated during the steering process (either alchemical or physical) can hinder the convergence of free energy estimators. Here, we discuss in depth this issue for the protein-ligand binding free energy estimation carried out via physical paths. We found that the water model and the parametrization of the path collective variables have a remarkable impact on the convergence rate of the estimators (e.g., Crooks). Finally, we provide practical recipes to enhance the convergence speed and minimize dissipation.
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Registered trials
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