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A term molecular mechanics refers to the apply of Newtonian mechanics to model molecular systems. Molecular mechanics approaches come widely applied within molecular structure filtration, molecular dynamics simulations, Monte Carlo simulations and ligand docking simulations.

Usually, molecular mechanics system consist of globose atoms attached by springs which represent bonds. Internal forces experient in the exemplary structure come described applying elementary 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 listing; numerous extra come available

[http://amber.scripps.edu/ AMBER] [http://www.charmm.org/ CHARMM forum] [http://www.igc.ethz.ch/gromos/ GROMOS] GROMACS [http://www.ks.uiuc.edu/Research/namd/ NAMD] [http://dasher.wustl.edu/tinker/ TINKER]

Molecular Mechanics
A tutorial published by the Center for Molecular Modeling of the U.S. National Institutes of Health.

Molecular Mechanics and Dynamics
Practical tutorial on the topic, including an overview of force field selection and applications.




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