Assessment of linear finite-difference poisson-boltzmann solvers

J. U N Wang, R. A Y Luo

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid, are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications.

Original languageEnglish (US)
Pages (from-to)1689-1698
Number of pages10
JournalJournal of Computational Chemistry
Volume31
Issue number8
DOIs
StatePublished - Jun 2010

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CPU Time
Poisson-Boltzmann Equation
Ludwig Boltzmann
Program processors
Boltzmann equation
Finite Difference
Siméon Denis Poisson
Cholesky
Conjugate Gradient
Linearly
Data storage equipment
Convergence Criteria
Biomolecules
Numerical Procedure
Test Set
Free Boundary
Comparative Analysis
Logarithm
Large Set
Electrostatics

Keywords

  • Electrostatic interaction
  • Finite difference
  • Implicit solvent
  • Numeric solver
  • Poisson-boltzmann equation

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Assessment of linear finite-difference poisson-boltzmann solvers. / Wang, J. U N; Luo, R. A Y.

In: Journal of Computational Chemistry, Vol. 31, No. 8, 06.2010, p. 1689-1698.

Research output: Contribution to journalArticle

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