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Quasi-Newton parallel geometry optimization methods

Source: J. Chem. Phys. 133, 034116 (2010); doi:10.1063/1.3455719

Published 20 July 2010

KEYWORDS and PACS
Keywords
PACS
  • 87.15.B-
    Structure of biomolecules
  • 87.14.ef
    Peptides
  • 33.15.Bh
    General molecular conformation and symmetry; stereochemistry
  • YEAR: 2010
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PUBLICATION DATA
ISSN:
1553-9628 (online)
Publisher:
AIP is a member of CrossRef AIP
Steven K. Burger and Paul W. Ayers
Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
Algorithms for parallel unconstrained minimization of molecular systems are examined. The overall framework of minimization is the same except for the choice of directions for updating the quasi-Newton Hessian. Ideally these directions are chosen so the updated Hessian gives steps that are same as using the Newton method. Three approaches to determine the directions for updating are presented: the straightforward approach of simply cycling through the Cartesian unit vectors (finite difference), a concurrent set of minimizations, and the Lanczos method. We show the importance of using preconditioning and a multiple secant update in these approaches. For the Lanczos algorithm, an initial set of directions is required to start the method, and a number of possibilities are explored. To test the methods we used the standard 50-dimensional analytic Rosenbrock function. Results are also reported for the histidine dipeptide, the isoleucine tripeptide, and cyclic adenosine monophosphate. All of these systems show a significant speed-up with the number of processors up to about eight processors. ©2010 American Institute of Physics
History: Received 4 January 2010; accepted 28 May 2010; published 20 July 2010
Permalink: http://link.aip.org/link/?JCPSA6/133/034116/1

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