Hybrid quantum mechanical/molecular mechanical approach to enzymatic reactions by utilizing the real-space grid technique

Takumi Hori, Hideaki Takahashi, Tomoshige Nitta

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

We have developed a novel quantum mechanical/molecular mechanical (QM/MM) code based on the real-space grids in order to realize high parallel efficiency. The details of the methodology and its parallel implementation have been presented. We have computed the electronic state of the QM subsystem using the Kohn-Sham density functional theory, where the one-electron wave functions have been expressed by the real-space grids distributed over a cubic cell. We have performed QM/MM simulations for the peptide hydrolysis in human immunodeficiency virus type-1 aspartyl protease in order to examine the reliability of the present QM/MM approach. The activation energy obtained by the present calculations shows a good agreement with the experimental results and that of the other QM/MM method. Finally, we have parallelized the whole code and found that the grid approach can afford high parallel efficiency (∼80%) in such a large scale electronic structure calculation. We conclude that the QM/MM approach utilizing real-space grids is adequate and efficient for the study of the enzymatic reactions.

Original languageEnglish
Pages (from-to)867-882
Number of pages16
JournalJournal of Theoretical and Computational Chemistry
Volume4
Issue number3
DOIs
Publication statusPublished - 2005 Sep 1
Externally publishedYes

Keywords

  • Enzymatic reactions
  • Human immunodeficiency virus type-1 aspartyl protease
  • Parallel computation
  • Quantum mechanical/molecular mechanical approach
  • Real-space grids

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics

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