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Abstract
Poisson-Boltzmann equation (PBE)-based implicit solvent models have been widely used in computational studies of biomolecules. The main difficulty for these models is how to set up the discretized equation near the solute-solvent interface. We have studied and implemented several new methods to improve its performance, including the second-order harmonic averaging method and the -factor harmonic averaging method. We specifically designed these new algorithms to have uniform banded structure for their discretized equations, so they would be more suitable for parallel computing and thus gain a tremendous efficiency on Graphical Processing Units (GPUs).
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