Numerical interpretation of molecular surface field in dielectric modeling of solvation
© 2017 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 38(2017), 14 vom: 30. Mai, Seite 1057-1070 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2017
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, N.I.H., Extramural Continuum Solvent Poisson-Boltzmann equation dielectric boundary force molecular surface Solvents |
| Zusammenfassung: | © 2017 Wiley Periodicals, Inc. Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one-dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface-to-atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second-order methods, including the one-dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one-dimensional method is far more efficient than standard second-order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc |
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| Beschreibung: | Date Completed 07.05.2019 Date Revised 26.03.2024 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.24782 |