ArticleJournal of chemical theory and computation2012
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.
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 12 papers.
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12 citing papers in PubMed.
- Fluctuating β-Sheet Secondary Structure in DS119 Explains the Small Effects of Backbone N-Amination on Thermal Stability.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.European biophysics journal : EBJ · 2022Article
- Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study.Frontiers in molecular biosciences · 2022Article
- Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.Journal of computational chemistry · 2018Article
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Journal of computational chemistry · 2017Article
- Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas.Journal of computer-aided molecular design · 2016Article
- Design and application of implicit solvent models in biomolecular simulations.Current opinion in structural biology · 2014Review
- Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.Journal of chemical theory and computation · 2013Article
- GSATools: analysis of allosteric communication and functional local motions using a structural alphabet.Bioinformatics (Oxford, England) · 2013Article
- Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization.Theoretical chemistry accountsArticle
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5 authors.
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Abstract
Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent-solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom-specific solvation parameter σ(i) (SASA). A procedure for the determination of values for the σ(i) (SASA) parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σ(i) (SASA) parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σ(g) (SASA) was obtained via partitioning of the atom-type σ(i) (SASA) distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces.
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