Development of o2p Software to Facilitate the Determination of Molecular Dynamics Simulation Parameters forMacromolecules with Repeating Units

• YABE Makoto

  Graduate School of Engineering, Yokohama National University,79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan

• SONOBE Chisaya

  Graduate School of Engineering, Yokohama National University,79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan

• UEDA Kazuyoshi

  Graduate School of Engineering, Yokohama National University,79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan

• TAKEDA Minoru

  Graduate School of Engineering, Yokohama National University,79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan

Bibliographic Information

Other Title

• 反復構造を持つ高分子に対する分子動力学計算のためのパラメータ設定支援プログラムo2pの開発

Abstract

Force field parameters required for molecular dynamics (MD) simulations can be obtained using quantum mechanical calculations, even if the parameters for a target molecule are unavailable from existing force fields. In the case of macromolecules, the derivation of parameters is difficult because of the high computational costs of the calculations. However, if the macromolecules of interest contain repeating units, the cost can be reduced using the following method. Initially, the parameters for an oligomer consisting of at least 3 repeating units (terminal and internal units) are obtained via quantum mechanical calculations. The parameters for the oligomer are then converted into the corresponding parameters for the polymer (terminal and internal × n units). The conversion from the oligomeric parameters to those of the polymer requires highly complicated multi-step procedures. In the present study, we developed web-based software (o2p) to facilitate the parameter conversion in a semi-automated manner using a simple graphical user interface. Its effectiveness was evaluated by conducting MD simulations for amylose in nonane. Spontaneous folding of amylose into a left-handed single helical structure was observed in the simulation. The resulting structure was in good agreement with experimental results, thereby demonstrating the effectiveness and reliability of o2p.

Journal

• Journal of Computer Chemistry, Japan

  Journal of Computer Chemistry, Japan 16 (3), 63-69, 2017

  Society of Computer Chemistry, Japan

Keywords

• Molecular dynamics simulation
• Macromolecules
• Parameters
• Gromacs
• Polymer
• Repeating unit

Details

• CRID: 1390282680154826624
• NII Article ID: 130006108680
• DOI: 10.2477/jccj.2017-0013
• ISSN: 13473824
• ISSN: 13471767
• Web Site: https://www.jstage.jst.go.jp/article/jccj/16/3/16_2017-0013/_pdf
• Text Lang: ja
• Data Source:
  • JaLC
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed