Inclusion of the most important multi-particle interactions in the amber force field and application of the revised force field to molecular dynamics calculations

N. K. Balabaev, S. A. Garbuzinskiy, O. V. Galzitskaya, A. V. Glyakina, B. T. Matkarimov, A. V. Finkelstein

Research output: Contribution to journalArticlepeer-review

Abstract

Formulas for calculation of energy and forces in the new force field of nonbonded interactions including along with traditional members, the polarization, induced by partial atomic charges, and three-particle dispersive interactions of the atoms with covalent bonds are received. The corresponding new members are added to a standard AMBER force field. Molecular dynamics calculations with the use of the updated force field are carried out. It is shown that additional physically reasonable members, taking into account the major three-particle interactions, not strongly slow down molecular dynamics simulation.

Original languageEnglish
Pages (from-to)427-435
Number of pages9
JournalMathematical Biology and Bioinformatics
Volume10
Issue number2
DOIs
Publication statusPublished - Jan 1 2015

Keywords

  • Interaction of atoms with covalent bonds
  • Non-bonded atom-atom interactions
  • Partial charges
  • Polarizability
  • Three-particle interactions

ASJC Scopus subject areas

  • Biomedical Engineering
  • Applied Mathematics

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