Molecular mechanics
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The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics simulations, Monte Carlo simulations and ligand docking simulations.
Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds. Internal forces experienced in the model structure are described using simple mathematical functions. Hooke's law is commonly used to describe bonded interactions and the atoms might be treated as inelastic hard-spheres or else they may interact according to the Lennard-Jones potential.
Software Packages
Limited list; many more are available
- AMBER (http://amber.scripps.edu/)
- CHARMM forum (http://www.charmm.org/)
- GROMOS (http://www.igc.ethz.ch/gromos/)
- NAMD (http://www.ks.uiuc.edu/Research/namd/)
- TINKER (http://dasher.wustl.edu/tinker/)
References
- U. Burkert and N.L. Allinger, Molecular Mechanics, 1982, ISBN 0841208859
- O. Becker, A.D. MacKerell, Jr., B. Roux and M. Watanabe, Editors, Computational Biochemistry and Biophysics, Marcel Dekker Inc., New York, 2001, ISBN 082470455X
- MacKerell, A.D., Jr., Empirical Force Fields for Biological Macromolecules: Overview and Issues, Journal of Computational Chemistry, 25: 1584-1604, 2004nl:moleculaire mechanica