ArticleJournal of chemical theory and computation2023
Improved Sampling of Adaptive Path Collective Variables by Stabilized Extended-System Dynamics.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Molecular Mechanism of ATP Hydrolysis Catalyzed by p97: A QM/MM Study.Journal of chemical theory and computation · 2025Article
- Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.Journal of chemical theory and computation · 2025Article
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Authors and funding
2 authors.
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Abstract
Because of the complicated multistep nature of many biocatalytic reactions, an a priori definition of reaction coordinates is difficult. Therefore, we apply enhanced sampling algorithms along with adaptive path collective variables (PCVs), which converge to the minimum free energy path (MFEP) during the simulation. We show how PCVs can be combined with the highly efficient well-tempered metadynamics extended-system adaptive biasing force (WTM-eABF) hybrid sampling algorithm, offering dramatically increased sampling efficiency due to its fast adaptation to path updates. For this purpose, we address discontinuities of PCVs that can arise due to path shortcutting or path updates with a novel stabilization algorithm for extended-system methods. In addition, we show how the convergence of simulations can be further accelerated by utilizing the multistate Bennett's acceptance ratio (MBAR) estimator. These methods are applied to the first step of the enzymatic reaction mechanism of pseudouridine synthases, where the ability of path WTM-eABF to efficiently explore intricate molecular transitions is demonstrated.
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Registered trials
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