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Molecular Dynamics Methods

  • I. Haneef

Abstract

Although macromolecules have been traditionally described in terms of rigid and unique three-dimensional structures, the dynamics of these molecules have become increasingly important in the understanding the relationships between structure and mechanism. It has been suggested that vibrational modes in macromolecules may act, for example, to channel energy from the solvent to the active site of an enzyme to enable the reaction pathway to proceed through the transition state. It has also been shown that the dynamics of a protein may be important in allowing the access of the substrate to enzyme and that changes in the vibrational modes may contribute to entropic terms affecting the free energy interactions.

Keywords

Configurational Space Free Energy Difference Force Evaluation Harmonic System Potential Function Versus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References And Further Reading

  1. Verlet L (1967), Phys Rev 159, 98CrossRefGoogle Scholar
  2. Gear C W (1971), `Numerical Initial Value Problems in Ordinary Differential Equations’, Prentice-HallGoogle Scholar
  3. Beeman D (1976), J Comp Phys 20 130Google Scholar

Copyright information

© Plenum Press, New York 1990

Authors and Affiliations

  • I. Haneef
    • 1
  1. 1.Astbury Department of BiophysicsUniversity of LeedsLeedsUK

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