Chem-Bio Informatics Journal
Online ISSN : 1347-0442
Print ISSN : 1347-6297
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Acceleration of monomer self-consistent charge process in fragment molecular orbital method
Takeshi IshikawaKazuo Kuwata
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JOURNALS FREE ACCESS

2010 Volume 10 Pages 24-31

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Abstract

We introduced the dynamic update technique into the monomer self-consistent charge (SCC) process of the fragment molecular orbital (FMO) method to reduce its computational costs. This technique has already been used for solving linear equations in some quantum chemical calculations. After performing test calculations on three typical polyglycines (GLY20, GLY40, and GLY60), we further performed the FMO calculations on the human immunodeficiency virus type 1 protease complexed with lopinavir using the dynamic update technique. These calculations demonstrate that the computational time of the monomer SCC process can be reduced by about one-third. Furthermore, we examined the dependence of the iteration number of the monomer SCC process on parallelization schemes.

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2010 Chem-Bio Informatics Society
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