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Matematicheskaya Biologiya i Bioinformatika, 2015, Volume 10, Issue 2, Pages 427–435
DOI: https://doi.org/10.17537/2015.10.427
(Mi mbb236)
 

This article is cited in 1 scientific paper (total in 1 paper)

Mathematical Modeling

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. Balabaeva, S. A. Garbuzinskiyb, O. V. Galzitskayab, A. V. Glyakinaa, B. T. Matkarimovc, A. V. Finkelsteinb

a Institute of Mathematical Problems of Biology, Pushchino, 142290, Russia
b Institute of Protein Research, Pushchino, Moscow Region, 142290 Russia
c National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
Full-text PDF (569 kB) Citations (1)
References:
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.
Received 26.10.2015, Published 05.11.2015
Document Type: Article
UDC: 577.1, 577.3, 54.03
Language: Russian
Citation: N. K. Balabaev, S. A. Garbuzinskiy, O. V. Galzitskaya, A. V. Glyakina, B. T. Matkarimov, A. V. Finkelstein, “Inclusion of the most important multi-particle interactions in the amber force field and application of the revised force field to molecular dynamics calculations”, Mat. Biolog. Bioinform., 10:2 (2015), 427–435
Citation in format AMSBIB
\Bibitem{BalGarGal15}
\by N.~K.~Balabaev, S.~A.~Garbuzinskiy, O.~V.~Galzitskaya, A.~V.~Glyakina, B.~T.~Matkarimov, A.~V.~Finkelstein
\paper Inclusion of the most important multi-particle interactions in the amber force field and application of the revised force field to molecular dynamics calculations
\jour Mat. Biolog. Bioinform.
\yr 2015
\vol 10
\issue 2
\pages 427--435
\mathnet{http://mi.mathnet.ru/mbb236}
\crossref{https://doi.org/10.17537/2015.10.427}
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  • https://www.mathnet.ru/eng/mbb/v10/i2/p427
  • This publication is cited in the following 1 articles:
    Citing articles in Google Scholar: Russian citations, English citations
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    Abstract page:183
    Full-text PDF :59
    References:47
     
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