Abstract
A fortran code PBSOLVE is created for numerical solution of a linear Poisson - Boltzman equation. Finite difference discretization and successive overrelaxation (SOR) iterations on the sequence of grids are used to obtain the approximate electrostatic potential on the grid. Error control is provided by comparison of solutions on nested grids. A parallel version of the PBSOLVE which exploits the message passing interface (MPI) has also been constructed. The performance of the program and the efficiency of parallelization have been tested on the small peptide Met-Enkephalin.
Chapter PDF
Similar content being viewed by others
References
C. Chotia, J. Janin, Nature 256 (1974) 705–708.
B. Honig, A. Nicholls, Science 268 (1995) 1144–1149.
B. Hingerty, R. H. Richie, T. L. Ferrel, J. Turner, Biopolymers 24 (1985) 427–439.
T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84 (1987) 3086–3090.
T. J. Richmond, J. Mol. Biol. 178 (1984) 63–89.
M. Connolly, J. Appl. Cryst. 16 (1983) 548.
F. Eisenhaber, et al, J. Comp. Chem. 16 (1995) 273–284.
M. K. Gilson, B. Honig, Biopolymers 25 (1986) 2097.
D. Jackson, Classical Electrodynamics (Wiley, New York, 1975).
M. Born, Z. Phys. 1 (1920) 45.
W. C. Still, W. A. Tempczyk, R. C. Hawley, T. J. Hendricson, J. Am. Chem. Soc. 112 (1990) 6127.
Di Qui, P. Shenkin, F.P. Hollinger, W.C. Still, J. Phys. Chem. A 101 (1997) 3005–3014.
B. N. Domany and Ch. L. Brooks III, J. Phys. Chem. B 103 (1999) 3765–3773.
F. Eisenmenger, U. Hansmann, Sh. Hayryan, C.-K. Hu, [SMMP] The Modern Package for Protein Simulations, to be submitted in 2000.
L.A. Hageman, D.M. Young, in: Applied Iterative Methods (Academic Press, New York, 1981).
M. Snir, et al, MPI (The MIT Press, Cambrage (USA), 1997).
D. Bai, A. Brandt, SIAM, J. Sci. Stat. Comput., 8 (1987) 109.
O.C. Zienkiewics, in: The Finite Element Method (McGraw-Hill, London, 1977).
C.A. Brebbia, J.C.F. Telles, L.C. Wrobel, in: Boundary Element Techniques: Theory and Applications in Engineering (Springer-Verlag, Berlin, 1984).
Sh. Hayryan, C.-K. Hu, S.-Y. Hu, R.-J. Shang, J. Comp. Chem., submitted.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hayryan, S., Hu, CK., Hayryan, E., Pokorny, I. (2003). Parallel Solution of the Poisson-Boltzmann Equation for Proteins. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Dongarra, J.J., Zomaya, A.Y., Gorbachev, Y.E. (eds) Computational Science — ICCS 2003. ICCS 2003. Lecture Notes in Computer Science, vol 2657. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44860-8_6
Download citation
DOI: https://doi.org/10.1007/3-540-44860-8_6
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-40194-0
Online ISBN: 978-3-540-44860-0
eBook Packages: Springer Book Archive