ArticleJournal of chemical theory and computation2012
Exact Relation between Potential of Mean Force and Free-Energy Profile.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Bayesian Umbrella Quadrature Automates Free-Energy Calculations Across Diverse Molecular Systems and Processes.Journal of chemical theory and computation · 2026Article
- Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.Biophysical journal · 2025Article
- Tutorial on Umbrella Sampling Simulation with a Combined QM/MM Potential: The Potential of Mean Force for an SThe journal of physical chemistry. B · 2024Article
- Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review.Journal of chemical information and modeling · 2021Review
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models.Journal of computational chemistry · 2014Article
- Spherical monovalent ions at aqueous liquid-vapor interfaces: interfacial stability and induced interface fluctuations.The journal of physical chemistry. B · 2013Article
- Liquid-vapor interfacial properties of aqueous solutions of guanidinium and methyl guanidinium chloride: influence of molecular orientation on interface fluctuations.The journal of physical chemistry. B · 2013Article
- Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions.The journal of physical chemistry. B · 2013Article
- Temperature dependence and energetics of single ions at the aqueous liquid-vapor interface.The journal of physical chemistry. B · 2013Article
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Authors and funding
2 authors.
Funding
Abstract
We apply concepts of covariant and contravariant vector space in differential geometry and general relativity to derive new, general, exact relations between potential of mean force and free-energy profile. These relations are immensely practical in free-energy simulations because a full Jacobian transformation (which is usually unknown) is not required; rather, only knowledge of the (constraint) coordinate of interest is needed. We reveal that in addition to the Jacobian determinant, the Jacobian scale factor and Leibnizian contributions must also be considered, as well a Fixman term with correct mass dependence. Our newly derived relations are verified with new non-trivial benchmark numerical examples for which exact results can be computed, and compared with relations available in the literature that turn out to exhibit significant deviations from the exact values.
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Registered trials
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