Parallel Processing of Molecular Geometry Parameter Optimization by Extended Huckel Method
-An Attempt of Simple Fast Generation of Molecular Structure -

Sumie TAJIMAa, Takahiro KATAGIRIb, Yasumasa KANADAc and Umpei NAGASHIMAd*

aDepartment of Humanculture and Science, Graduate School of Ochanomizu University
2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
bDepartment of Information Science, Graduate School of Science, the University of Tokyo
2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8658, Japan
cComputer Centre Division,Information Technology Center, the University of Tokyo
2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8658, Japan
dNational Institute for Interdisciplinary Research
1-1-4 Higashi, Tsukuba, Ibaraki 305-8562, Japan

(Received: November 29, 1999; Accepted for publication: December 27, 1999; Published on Web: April 10, 2000)

In order to have an initial molecular geometry simply and fast, we modified the extended Huckel method and developed a geometry optimize method using only total energy. The difference between calculated and observed values of small hydrocabon molecules is less than about 10%.
Parallel processing of the extended Huckel is very efficient up to 8 PC-cluster system because the efficiency for the extended Huckel calculation of DNA(115 atoms and 286 dimension) is bigger than 90%.

Keywords: Extended Huckel method, Molecular Geometry Optimization, Matrix Diagonalization, Parallel Processing, PC Cluster

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