ArticleThe journal of physical chemistry letters2013
Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.
Article in The journal of physical chemistry letters, 2013. 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.
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework.The journal of physical chemistry. A · 2026Article
- Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats.Nucleic acids research · 2022Article
- Computational Indicator Approach for Assessment of Nanotoxicity of Two-Dimensional Nanomaterials.Nanomaterials (Basel, Switzerland) · 2022Article
- Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel.Computational and structural biotechnology journal · 2022Article
- Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Redox-coupled quinone dynamics in the respiratory complex I.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.Journal of the American Chemical Society · 2017Article
- Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.Journal of chemical theory and computation · 2015Article
- Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter.Nature communications · 2015Article
- Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.Journal of chemical theory and computation · 2015Article
- Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach.Molecular membrane biology · 2015Article
- Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.Journal of chemical theory and computation · 2014Article
- Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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Authors and funding
2 authors.
Funding
Abstract
We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.
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Registered trials
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