ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
A series of different simplifications of the boundary element method (BEM) for solving the Poisson–Boltzmann equation is investigated in an effort to obtain an accurate and fast enough treatment of electrostatic effects to be incorporated in Monte-Carlo and molecular dynamics simulation methods. The tested simplifications include increasing the size of Boundary Elements, decreasing the surface dot density, and ignoring the interactions between the polarization charges. Combined with terms describing the nonelectrostatic solvation effects, the simplified BEM polarization terms were built into expressions for the solvation potential. The solvation potential is treated as empirical consistent force field equations. The intervening parameters, including atomic and probe radii, are derived by different fitting strategies of calculated vs experimental vacuum to water transfer energies of 173 charged, polar, and nonpolar small molecules. These fits are shown to yield very good correlations (rms ∼1.4 kcal/mol), even when the interactions between the polarization charges are neglected, proving that the most time-consuming step in BEM, which involves solving the linear system, can be successfully avoided. Finally, the computing efficiency of the method is tested on macromolecules and is found to be convenient for implementation in molecular dynamics or Monte Carlo simulations. © 1996 American Institute of Physics.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.471386
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