DOI: 10.1002/jcc.540120718. Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence

Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence

10.1002/jcc.540120718

Crossref journal-article

Wiley

Journal of Computational Chemistry (311)

Abstract

AbstractFinite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.

Bibliography

Davis, M. E., & McCammon, J. A. (1991). Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence. Journal of Computational Chemistry, 12(7), 909â912. Portico.

Authors 2

Malcolm E. Davis (first)
J. Andrew McCammon (additional)

References 13 Referenced 108

10.1016/0022-2836(85)90248-7
10.1126/science.2838904
10.1021/j100358a002
10.1073/pnas.86.5.1524
10.1016/0022-2836(89)90487-7
10.1073/pnas.86.14.5361
10.1021/bi00492a014
10.1021/bi00496a010
10.1021/cr00101a005
10.1146/annurev.bb.19.060190.001505 / Ann. Rev. Biophys. Biophysical Chem. by Sharp K. A. (1990)
{'key': 'e_1_2_1_12_2', 'volume-title': 'Biophysical Chemistry: Parts I, II, and III.', 'author': 'Cantor C. R.', 'year': '1980'} / Biophysical Chemistry: Parts I, II, and III. by Cantor C. R. (1980)
10.1002/prot.340010109
10.1080/00268978400102061

Dates

Type	When
Created	20 years, 7 months ago (Jan. 1, 2005, 7:36 p.m.)
Deposited	1 year, 9 months ago (Oct. 22, 2023, 7:26 p.m.)
Indexed	2 months, 2 weeks ago (June 6, 2025, 5:08 a.m.)
Issued	33 years, 11 months ago (Sept. 1, 1991)
Published	33 years, 11 months ago (Sept. 1, 1991)
Published Online	20 years, 11 months ago (Sept. 7, 2004)
Published Print	33 years, 11 months ago (Sept. 1, 1991)

Funders 0

None

BibTeX

@article{Davis_1991, title={Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence}, volume={12}, ISSN={1096-987X}, url={http://dx.doi.org/10.1002/jcc.540120718}, DOI={10.1002/jcc.540120718}, number={7}, journal={Journal of Computational Chemistry}, publisher={Wiley}, author={Davis, Malcolm E. and McCammon, J. Andrew}, year={1991}, month=sep, pages={909–912} }

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