Systematic study of the boundary composition in Poisson Boltzmann calculations

  1. Parimal Kar1,
  2. Yanjie Wei1,
  3. Ulrich H. E. Hansmann1,2,
  4. Siegfried Höfinger1,*

Article first published online: 14 MAY 2007

DOI: 10.1002/jcc.20698

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 28, Issue 16, pages 2538–2544, December 2007

Additional Information

How to Cite

Kar, P., Wei, Y., Hansmann, U. H. E. and Höfinger, S. (2007), Systematic study of the boundary composition in Poisson Boltzmann calculations. Journal of Computational Chemistry, 28: 2538–2544. doi: 10.1002/jcc.20698

Author Information

  1. 1

    Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, 49331-1295

  2. 2

    John v. Neumann Institute for Computing, Forschungszentrum Jülich, 52425 Jülich, Germany

*Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, 49331-1295

Publication History

  1. Issue published online: 12 OCT 2007
  2. Article first published online: 14 MAY 2007
  3. Manuscript Accepted: 10 JAN 2007
  4. Manuscript Received: 12 DEC 2006

Funded by

  • National Institutes of Health Grants. Grant Number: GM62838
  • National Science Foundation. Grant Number: CHE-0313618

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Keywords:

  • solvation;
  • continuum electrostatics;
  • polarizable continuum model;
  • Poisson Boltzmann;
  • implicit solvation models

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Abstract

We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but our results are also of interest to finite difference techniques of Poisson Boltzmann calculations. At first, we identify the critical size of the geometrical elements for discretizing the boundary, and thus the necessary resolution required to establish numerical convergence.

In the following two steps we perform reference calculations on a set of dipeptides in different conformations using the Polarizable Continuum Model and a high-level Density Functional as well as a high-quality basis set. Afterwards, we propose a mechanism for defining appropriate boundary geometries. Finally, we compare the classic Poisson Boltzmann description with the Quantum Chemical description, and aim at finding appropriate fitting parameters to get a close match to the reference data. Surprisingly, when using default AMBER partial charges and the rigorous geometric parameters derived in the initial two stages, no scaling of the partial charges is necessary and the best fit against the reference set is obtained automatically. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

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