Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme

Toshiki Nagai, Ayori Mitsutake, Hiroshi Takano

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

Original languageEnglish
Article number023803
JournalJournal of the Physical Society of Japan
Volume82
Issue number2
DOIs
Publication statusPublished - 2013 Feb 1

Keywords

  • Molecular dynamics
  • Principal component analysis
  • Protein
  • Relaxation mode analysis
  • Simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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