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

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4 Author(s)
Baker, N.A. ; Departments of Chemistry and Biochemistry and of Mathematics, University of California at San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, 92093, USA ; Sept, D. ; Holst, M.J. ; McCammon, J.A.

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.

Note: The Institute of Electrical and Electronics Engineers, Incorporated is distributing this Article with permission of the International Business Machines Corporation (IBM) who is the exclusive owner. The recipient of this Article may not assign, sublicense, lease, rent or otherwise transfer, reproduce, prepare derivative works, publicly display or perform, or distribute the Article.  

Published in:

IBM Journal of Research and Development  (Volume:45 ,  Issue: 3.4 )