Russian version English version
Volume 10   Issue 2   Year 2015
Inclusion of the Most Important Multi-Particle Interactions in the Amber Force Field and Application of the Revised Force Field To Molecular Dynamics Calculations

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

Institute of Mathematical Problems of Biology, Pushchino, 142290, Russia
Institute of Protein Research, Pushchino, Moscow Region, 142290 Russia
National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan

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.
Key words: non-bonded atom-atom interactions, three-particle interactions, polarizability, partial charges, interaction of atoms with covalent bonds.
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2015.10.427
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


  Copyright IMPB RAS © 2005-2024