ArticleJournal of chemical theory and computation2012
Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
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- Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein.The journal of physical chemistry. B · 2022Article
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Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Grid dependence in numerical reaction field energies and solvation forces is a well-known limitation in the finite-difference Poisson-Boltzmann methods. In this study we have investigated several numerical strategies to overcome the limitation. Specifically, we have included trimer arc dots during analytical molecular surface generation to improve the convergence of numerical reaction field energies and solvation forces. We have also utilized the level set function to trace the molecular surface implicitly to simplify the numerical mapping of the grid-independent solvent excluded surface. We have further explored to combine the weighted harmonic averaging of boundary dielectrics with a charge-based approach to improve the convergence and stability of numerical reaction field energies and solvation forces. Our test data show that the convergence and stability in both numerical energies and forces can be improved significantly when the combined strategy is applied to either the Poisson equation or the full Poisson-Boltzmann equation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.