An efficient local molecular dynamics polymerization simulation combined with an ab initio MO method

Peng Xie, Yuuichi Orimoto, Yuriko Aoki

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom's nucleus in the active region are calculated by the ELG method while the equations of the nucleus's motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly induced by the hydrogen bonds observed in two types of H-bond rings.

Original languageEnglish
Pages (from-to)870-885
Number of pages16
JournalMaterials
Volume6
Issue number3
DOIs
Publication statusPublished - Apr 9 2013

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Molecular dynamics
Elongation
Polymerization
Gears
Water
Computer simulation
Conformations
Hydrogen bonds
Polymers
Atoms
Molecules
polyglycine

All Science Journal Classification (ASJC) codes

  • Materials Science(all)

Cite this

An efficient local molecular dynamics polymerization simulation combined with an ab initio MO method. / Xie, Peng; Orimoto, Yuuichi; Aoki, Yuriko.

In: Materials, Vol. 6, No. 3, 09.04.2013, p. 870-885.

Research output: Contribution to journalArticle

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