Acceleration of monomer self-consistent charge process in fragment molecular orbital method

• Ishikawa Takeshi

  Division of Prion Research, Center for Emerging Infectious Disease Gifu University CREST Project, Japan Science and Technology Agency,

• Kuwata Kazuo

  Division of Prion Research, Center for Emerging Infectious Disease Gifu University CREST Project, Japan Science and Technology Agency,

Bibliographic Information

Other Title

• フラグメント分子軌道法におけるモノマーSCC計算の高速化

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.

Journal

• Chem-Bio Informatics Journal

  Chem-Bio Informatics Journal 10 24-31, 2010

  Chem-Bio Informatics Society

Keywords

• Fragment molecular orbital method
• monomer self-consistent charge process
• dynamic update
• HIV-1 protease

Details

• CRID: 1390001205103271936
• NII Article ID: 130004138110
• DOI: 10.1273/cbij.10.24
• ISSN: 13470442
• ISSN: 13476297
• Web Site: http://www.jstage.jst.go.jp/article/cbij/10/0/10_0_24/_pdf
• Data Source:
  • JaLC
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed