Geometry Optimization of Kringle 1 of Plasminogen Using the PM3 Semiempirical Method

Andrew D. Daniels, Gustavo E. Scuseria, O. Farkas, H. Bernhard Schlegel

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The results of a geometry optimization on the 1226 atom Kringle 1 of plasminogen are presented. The energy and gradients were calculated using a linear-scaling PM3 semiempirical method with a conjugate gradient density matrix search replacing the diagonalization step. The geometry was optimized with the rational function optimization technique combined with a modified version of the direct inversion in the iterative subspace procedure. The optimization required 362 geometry update steps to reach a local minimum. An analysis is given of the optimization and timing results using a single processor on the SGI Origin2000.

Original languageEnglish
Pages (from-to)82-89
Number of pages8
JournalInternational Journal of Quantum Chemistry
Volume77
Issue number1
Publication statusPublished - Mar 5 2000

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Plasminogen
optimization
Geometry
geometry
rational functions
gradients
Rational functions
central processing units
time measurement
inversions
scaling
Atoms
atoms
energy

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Geometry Optimization of Kringle 1 of Plasminogen Using the PM3 Semiempirical Method. / Daniels, Andrew D.; Scuseria, Gustavo E.; Farkas, O.; Schlegel, H. Bernhard.

In: International Journal of Quantum Chemistry, Vol. 77, No. 1, 05.03.2000, p. 82-89.

Research output: Contribution to journalArticle

Daniels, Andrew D. ; Scuseria, Gustavo E. ; Farkas, O. ; Schlegel, H. Bernhard. / Geometry Optimization of Kringle 1 of Plasminogen Using the PM3 Semiempirical Method. In: International Journal of Quantum Chemistry. 2000 ; Vol. 77, No. 1. pp. 82-89.
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