The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers

Authors:
N. A. Baker;D. Sept;M. J. Holst;J. A. McCammon
Affiliations:
Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California and Department of Mathematics, University of California at San Diego, La Jolla, California;Department of Biomedical Engineering, Washington University, St. Louis, Missouri;Department of Mathematics, University of California at San Diego, La Jolla, California;Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California and Departments of Pharmacology, University of California at San Diego, La Jolla, California
Venue:
IBM Journal of Research and Development
Year:
2001

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Abstract

By using new methods for the parallel solution of elliptic partial differential equations, the teraflops computing power of massively parallel computers can be leveraged to perform electrostatic calculations on large biological systems. This paper describes the adaptive multilevel finite element solution of the Poisson-Boltzmann equation for a microtubule on the NPACI Blue Horizon--a massively parallel IBM RS/6000® SP with eight POWER3 SMP nodes. The microtubule system is 40 nm in length and 24 nm in diameter, consists of roughly 600000 atoms, and has a net charge of -1800 e. Poisson-Boltzmann calculations are performed for several processor configurations, and the algorithm used shows excellent parallel scaling.