Accuracy of dimer-es approximation on fragment molecular orbital (Fmo) method

Tatsuya Nakano, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe, Yuto Komeiji, Yuji Mochizuki

Research output: Contribution to journalArticle

Abstract

The fragment molecular orbital (FMO) method is recently attracting attention as a method of calculating the electronic state of macromolecular systems. To enhance the speed of the FMO method, it is necessary to apply an approximation in which SCF calculations are neglected for distant fragment (monomer) pairs (dimers) and instead the electrostatic interactions between the two monomers are calculated. This approximation is called the dimer-es approximation. The accuracy and speed brought by the dimer-es approximation depend on the minimum threshold distance between two atoms to apply the approximation. This threshold distance given in unit of van der Waals radii is named “Ldimer-es”. In this communication, we examined dependence of HF and MP2 electron correlation energy errors on “Ldimer-es”, and it is preferable to calculate FMO4-HF and FMO4-MP2 for calculation of FMO-HF and FMO-MP2 of side chain-split peptides with Ldimer-es=2.0.

Original languageEnglish
Pages (from-to)119-122
Number of pages4
JournalChem-Bio Informatics Journal
Volume18
DOIs
Publication statusPublished - 2018

Keywords

  • Dimer-es approximation
  • Fragment molecular orbital
  • Many-body fmo method
  • Side chain fragmentation

ASJC Scopus subject areas

  • Biochemistry

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