Paper Citing NAMD - Abstract
Bardhan, Jaydeep P.; Knepley, Matthew G.
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 124107, SEP 28 2011
We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics, using the analytically solvable case of a spherical solute containing an arbitrary charge distribution. Our analysis, which builds on Kirkwood's solution using spherical harmonics, clarifies important aspects of the approximation and its relationship to generalized Born models. First, our results suggest a new perspective for analyzing fast electrostatic models: the separation of variables between material properties (the dielectric constants) and geometry (the solute dielectric boundary and charge distribution). Second, we find that the eigenfunctions of the reaction-potential operator are exactly preserved in the BIBEE model for the sphere, which supports the use of this approximation for analyzing charge-charge interactions in molecular binding. Third, a comparison of BIBEE to the recent GB epsilon theory suggests a modified BIBEE model capable of predicting electrostatic solvation free energies to within 4% of a full numerical Poisson calculation. This modified model leads to a projection-framework understanding of BIBEE and suggests opportunities for future improvements. (C) 2011 American Institute of Physics. [doi:10.1063/1.3641485]
