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Poisson-Boltzmann (PB) model is one of the most popular implicit solventmodels in biophysical modeling and computation. The ability of providingaccurate and reliable PB estimation of electrostatic solvation free energy,$\Delta G_{\text{el}}$, and binding free energy, $\Delta\Delta G_{\text{el}}$,is of tremendous significance to computational biophysics and biochemistry.Recently, it has been warned in the literature (Journal of Chemical Theory andComputation 2013, 9, 3677-3685) that the widely used grid spacing of $0.5$ \AA$ $ produces unacceptable errors in $\Delta\Delta G_{\text{el}}$ estimationwith the solvent exclude surface (SES). In this work, we investigate the griddependence of our PB solver (MIBPB) with SESs for estimating both electrostaticsolvation free energies and electrostatic binding free energies. It is foundthat the relative absolute error of $\Delta G_{\text{el}}$ obtained at the gridspacing of $1.0$ \AA $ $ compared to $\Delta G_{\text{el}}$ at $0.2$ \AA $ $averaged over 153 molecules is less than 0.2\%. Our results indicate that theuse of grid spacing $0.6$ \AA $ $ ensures accuracy and reliability in$\Delta\Delta G_{\text{el}}$ calculation. In fact, the grid spacing of $1.1$\AA $ $ appears to deliver adequate accuracy for high throughput screening.

Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies