Figure 3.

An example of an equation used to approximate the atomic forces that govern molecular movement. The atomic forces that govern molecular movement can be divided into those caused by interactions between atoms that are chemically bonded to one another and those caused by interactions between atoms that are not bonded. Chemical bonds and atomic angles are modeled using simple springs, and dihedral angles (that is, rotations about a bond) are modeled using a sinusoidal function that approximates the energy differences between eclipsed and staggered conformations. Non-bonded forces arise due to van der Waals interactions, modeled using the Lennard-Jones potential, and charged (electrostatic) interactions, modeled using Coulomb's law.

Durrant and McCammon BMC Biology 2011 9:71   doi:10.1186/1741-7007-9-71
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