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.
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