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Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
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10.1063/1.3641485
/content/aip/journal/jcp/135/12/10.1063/1.3641485
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/12/10.1063/1.3641485

Figures

Image of FIG. 1.
FIG. 1.

A diagram of the mixed-dielectric Poisson model, showing two discrete point charges in the solute.

Image of FIG. 2.
FIG. 2.

Modifying BIBEE using BIBEE/CFA for the monopole moment and BIBEE/P provides a tighter lower bound for charged molecules. (a) Correlation plot of the BIBEE estimated electrostatic solvation free energies, for multiple sets of 25 randomly located point charges in a sphere of radius 5 Å, with dielectric constants ε1 = 4 and ε2 = 80. Results labeled BEM BIBEE/M illustrate the same model computed using the BEM implementation of BIBEE, i.e., a numerical method suitable for arbitrary geometries. (b) Correlation plot of the improved BIBEE estimates for electrostatic solvation free energies for 200 proteins from the test set of Feig et al. (Ref. 68), using CHARMM22 radii and charges, and dielectric constants ε1 = 4 and ε2 = 80.

Image of FIG. 3.
FIG. 3.

Dependence of modified BIBEE model accuracy on the eigenvalue approximation, taken over 50 structures from the test set of Feig et al. (Ref. 68) using CHARMM22 radii and charges, and dielectric constants ε1 = 4 and ε2 = 80.

Image of FIG. 4.
FIG. 4.

Electrostatic solvation free energies for all of the proteins from the test set of Feig et al. (Ref. 68), using CHARMM22 radii and charges, and dielectric constants ε1 = 4 and ε2 = 80, the original BIBEE/CFA and BIBEE/P models, as well as the modified BIBEE with the eigenvalue approximation λ = −0.20.

Image of FIG. 5.
FIG. 5.

Electrostatic solvation free energies for 50 structures of met-enkephalin taken from an all-atom molecular dynamics simulation in explicit water. The GBMV results were calculated using CHARMM (Ref. 8) and the remainder were calculated using ε1 = 1, ε2 = 80, and CHARMM22 radii and charges. See text for other calculation details.

Tables

Generic image for table
Table I.

Dependence of modified BIBEE model accuracy on the eigenvalue approximation, taken over 50 structures from the test set of Feig et al. (Ref. 68). See main text for calculation details.

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/content/aip/journal/jcp/135/12/10.1063/1.3641485
2011-09-28
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/12/10.1063/1.3641485
10.1063/1.3641485
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