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 methods to overcome the difficulty, including classic methods, such as the classical harmonic averaging, and those we recently developed, such as second-order harmonic averaging and immersed interface method. We were able to identify some key factors, which are interface properties, that are closely related to the performance of the methods. For example, an extremely important one is what we call “X-factor” in our study, whose average value would directly determine the reaction field energy results. Another one, deviation integral, also is shown to be critical for a model in terms of its convergence against grid spacing. By carefully dealing with these interface properties, we showed that the performance of the methods can be drastically improved. Moreover, the practical grid spacing used for current PB models may be greatly increased, from 0.5 Å to about 1 Å.

Improving Poisson-Boltzmann modeling by utilizing more physical interface properties

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.