ArticleJournal of chemical theory and computation2015
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Fast sampling of protein conformational dynamics.Science advances · 2026Article
- Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton.Cytoskeleton (Hoboken, N.J.) · 2024Article
- Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.Journal of chemical theory and computation · 2024Article
- Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.Journal of chemical theory and computation · 2024Article
- Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.Journal of chemical theory and computation · 2023Article
- Article
- Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.Journal of chemical theory and computation · 2022Article
- Computational methods for exploring protein conformations.Biochemical Society transactions · 2020Review
- Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.The journal of physical chemistry. B · 2020Article
- Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.The Journal of chemical physics · 2018Article
- Article
- Comparison of mechanistic transport cycle models of ABC exporters.Biochimica et biophysica acta. Biomembranes · 2018Review
- Coarse-Grained Directed Simulation.Journal of chemical theory and computation · 2017Article
- Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics.Journal of chemical theory and computation · 2017Article
- A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.The Journal of chemical physics · 2016Article
- Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.Methods in enzymology · 2016Review
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4 authors.
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Abstract
Metadynamics is an enhanced sampling method designed to flatten free energy surfaces uniformly. However, the highest-energy regions are often irrelevant to study and dangerous to explore because systems often change irreversibly in unforeseen ways in response to driving forces in these regions, spoiling the sampling. Introducing an on-the-fly domain restriction allows metadynamics to flatten only up to a specified energy level and no further, improving efficiency and safety while decreasing the pressure on practitioners to design collective variables that are robust to otherwise irrelevant high energy driving. This paper describes a new method that achieves this using sequential on-the-fly estimation of energy wells and redefinition of the metadynamics hill shape, termed metabasin metadynamics. The energy level may be defined a priori or relative to unknown barrier energies estimated on-the-fly. Altering only the hill ensures that the method is compatible with many other advances in metadynamics methodology. The hill shape has a natural interpretation in terms of multiscale dynamics, and the computational overhead in simulation is minimal when studying systems of any reasonable size, for instance proteins or other macromolecules. Three example applications show that the formula is accurate and robust to complex dynamics, making metadynamics significantly more forgiving with respect to CV quality and thus more feasible to apply to the most challenging biomolecular systems.
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