Improving Generalized Born Models by Exploiting Connections to Polarizable Continuum Models. I. An Improved Effective Coulomb Operator

Lange, Adrian W.; Herbert, John M.

doi:10.1021/ct300111m

Cited by 31 publications

(65 citation statements)

References 64 publications

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“…A substantially different form of the GB kernel fijGB was recently proposed(59), based on a carefully examined connection between the GB and conductor-like polarizable continuum models(117): fij=rij+(1+1.028rij16RiRj)−16 Noticeable improvements over the canonical GB in both accuracy and speed were reported(59), however the testing was so far limited to either the perfect or R6 effective Born radii.…”

Section: Polar Solvation: the Generalized Born Modelmentioning

confidence: 99%

Generalized Born Implicit Solvent Models for Biomolecules

Onufriev

Case

2019

Annu. Rev. Biophys.

208

210

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It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.

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Section: Polar Solvation: the Generalized Born Modelmentioning

confidence: 99%

Generalized Born Implicit Solvent Models for Biomolecules

Onufriev

Case

2019

Annu. Rev. Biophys.

208

210

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“…Several computationally efficient adaptations/approximations of the general ASC formalism, notably many variants of Polarizable Continuum Model (PCM), e.g., COSMO, are widely used in computational chemistry to model solvation effects, see Ref for a comprehensive review. Some of these approximations are conceptually equivalent to the GB model …”

Section: Implicit Solvent Modelsmentioning

confidence: 99%

“…A great variety of flavors and implementations of the GB are available, several of which implemented in molecular modeling packages such as AMBER, CHARMM, GROMACS, NAMD, OpenMM, or TINKER . The specific choice depends on specific needs: a protein folding simulation may call for one flavor of the GB model, while a study of a protein in a membrane environment will need quite another .…”

Section: Implicit Solvent Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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“…There are good reasons to be skeptical of any "universal" definition based on a set of atomic radii. From a theoretical point of view, careful examination of the Born ion model 46 and the generalized Born (GB) formalism 152,153 suggests that the cavity radius is not strictly a property of the solute but ought to depend on the dielectric constant as well, and probably also on temperature 248 . A universal set of radii cannot capture changes in atomic size with respect to oxidation state, although empirical schemes have been suggested to modify the radii based on atomic charge 150,151 .…”

Section: Methodsmentioning

confidence: 99%

“…Beyond that, there is little theoretical justification for any of them, and no guarantee that small changes in the atomic radii will not have a significant impact on computed observables 113,149 . It has been suggested that the “optimal” atomic radius for a given atom likely ought to vary as a function of its partial atomic charge, 150,151 and probably as a function of the solvent's dielectric constant as well 94,132,152,153 . In quantum chemistry, the latter effect is generally neglected whereas the former is handled empirically, if at all.…”

Section: Continuum Electrostaticsmentioning

confidence: 99%

Dielectric continuum methods for quantum chemistry

Herbert

2021

WIREs Comput Mol Sci

Self Cite

142

195

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This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular boundary‐element approach to the problem defined by the Poisson or Poisson–Boltzmann equation, but that moniker belies the diversity of available methods. This work reviews the current state‐of‐the art, with emphasis on theory and methods rather than applications. The basics of continuum electrostatics are described, including the nonequilibrium polarization response upon excitation or ionization of the solute. Nonelectrostatic interactions, which must be included in the model in order to obtain accurate solvation energies, are also described. Numerical techniques for implementing the equations are discussed, including linear‐scaling algorithms that can be used in classical or mixed quantum/classical biomolecular electrostatics calculations. Anisotropic models that can describe interfacial solvation are briefly described. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Molecular and Statistical Mechanics > Free Energy Methods

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Improving Generalized Born Models by Exploiting Connections to Polarizable Continuum Models. I. An Improved Effective Coulomb Operator

Cited by 31 publications

References 64 publications

Generalized Born Implicit Solvent Models for Biomolecules

Generalized Born Implicit Solvent Models for Biomolecules

Water models for biomolecular simulations

Dielectric continuum methods for quantum chemistry

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