An efficient second-order poisson-boltzmann method
© 2019 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 40(2019), 12 vom: 05. Mai, Seite 1257-1269 |
|---|---|
| 1. Verfasser: | |
| Weitere Verfasser: | , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2019
|
| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Proteins Water 059QF0KO0R |
| Zusammenfassung: | © 2019 Wiley Periodicals, Inc. Immersed interface method (IIM) is a promising high-accuracy numerical scheme for the Poisson-Boltzmann model that has been widely used to study electrostatic interactions in biomolecules. However, the IIM suffers from instability and slow convergence for typical applications. In this study, we introduced both analytical interface and surface regulation into IIM to address these issues. The analytical interface setup leads to better accuracy and its convergence closely follows a quadratic manner as predicted by theory. The surface regulation further speeds up the convergence for nontrivial biomolecules. In addition, uncertainties of the numerical energies for tested systems are also reduced by about half. More interestingly, the analytical setup significantly improves the linear solver efficiency and stability by generating more precise and better-conditioned linear systems. Finally, we implemented the bottleneck linear system solver on GPUs to further improve the efficiency of the method, so it can be widely used for practical biomolecular applications. © 2019 Wiley Periodicals, Inc |
|---|---|
| Beschreibung: | Date Completed 10.08.2020 Date Revised 05.08.2023 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.25783 |