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- W2070126787 abstract "Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson–Boltzmann equation for electrostatic analyses of realistic biomolecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field." @default.
- W2070126787 created "2016-06-24" @default.
- W2070126787 creator A5032088629 @default.
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- W2070126787 creator A5063315556 @default.
- W2070126787 creator A5065809572 @default.
- W2070126787 creator A5069922005 @default.
- W2070126787 date "2013-11-01" @default.
- W2070126787 modified "2023-10-13" @default.
- W2070126787 title "Exploring accurate Poisson–Boltzmann methods for biomolecular simulations" @default.
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- W2070126787 doi "https://doi.org/10.1016/j.comptc.2013.09.021" @default.
- W2070126787 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3891588" @default.
- W2070126787 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24443709" @default.
- W2070126787 hasPublicationYear "2013" @default.