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Molecular Mechanics

  • Philipp O. J. Scherer
Part of the Graduate Texts in Physics book series (GTP)

Abstract

Classical molecular mechanics simulations have become a very valuable tool for the investigation of atomic and molecular systems, mainly in the area of materials science and molecular biophysics. They use a classical energy function which treats the atoms as mass points interacting by classical forces. Simulations of larger molecules use empirical force fields, which approximate the potential energy surface of the electronic ground state. We discuss the most important interaction terms, which are conveniently expressed in internal coordinates, i.e. bond lengths, bond angles and dihedral angles. We derive expressions for the gradients of the force field with respect to Cartesian coordinates. In a computer experiment we simulate a glycine dipeptide and demonstrate the principles of energy minimization, normal mode analysis of small amplitude motions around an equilibrium geometry and the simulation of molecular dynamics.

Keywords

Force Field Dihedral Angle Normal Mode Analysis Classical Molecular Dynamic Simulation Torsional Potential 
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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Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • Philipp O. J. Scherer
    • 1
  1. 1.Physikdepartment T38Technische Universität MünchenGarchingGermany

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