Harmonic vibrational analysis in delocalized internal coordinates

Frank Jensen, David S. Palmer

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

It is shown that a principal component analysis of a large set of internal coordinates can be used to define a nonredundant set of delocalized internal coordinates suitable for the calculation of harmonic vibrational normal modes. The selection of internal coordinates and the principal component analysis provide large degrees of freedom in extracting a nonredundant set of coordinates, and thus influence how the vibrational normal modes are described. It is shown that long-range coordinates may be especially suitable for describing low-frequency global deformation modes in proteins.
LanguageEnglish
Pages223-230
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume7
Issue number1
DOIs
Publication statusPublished - 2011

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Principal component analysis
harmonics
principal components analysis
Proteins
degrees of freedom
low frequencies
proteins

Keywords

  • vibrational analysis
  • internal coordinates

Cite this

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Harmonic vibrational analysis in delocalized internal coordinates. / Jensen, Frank; Palmer, David S.

In: Journal of Chemical Theory and Computation , Vol. 7, No. 1, 2011, p. 223-230.

Research output: Contribution to journalArticle

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AB - It is shown that a principal component analysis of a large set of internal coordinates can be used to define a nonredundant set of delocalized internal coordinates suitable for the calculation of harmonic vibrational normal modes. The selection of internal coordinates and the principal component analysis provide large degrees of freedom in extracting a nonredundant set of coordinates, and thus influence how the vibrational normal modes are described. It is shown that long-range coordinates may be especially suitable for describing low-frequency global deformation modes in proteins.

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