Numerical Difficulties Computing Electrostatic Potentials Near Interfaces with the Poisson-Boltzmann Equation

Many researchers compute surface maps of the electrostatic potential (φ) with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of φ, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of φ) at the surface. The Cartesian Poisson-Boltzmann solver contains several features that reduce the numerical noise in surface maps of φ: First, CPB introduces additional mesh points at the Cartesian grid/surface intersections where the PB equation is solved. This procedure ensures that the solution for interior mesh points only references nodes on the interior or on the surfaces; similarly for exterior points. Second, for added points on the surface, a second order least-squares reconstruction (LSR) is implemented that analytically incorporates the discontinuities at the surface. LSR is used both during the solution phase to compute φ at the surface and during postprocessing to obtain φ, induced charges, and ionic pressures. Third, it uses an adaptive grid where the finest grid cells are located near the molecular surface.