Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online



F.  Summary Interactions

Some programs assign charges using rules or templates, especially for macromolecules. In some force-fields, the torsional potential is calibrated to a particular charge calculation method (rarely made known to the user). Use of a different method can invalidated the force-field consistency.  Sometimes, an additional bonded interaction term, improper dihedrals, are added as illustrated below.  The potential for that is given by the following equation:

Eimproper = Σangles kω (ω - ωo)2

  All of the potential energy functions are illustrated in the graph below, where V is the potential energy.

Go to this great web site by Sharon Hammes-Schiffer, Shaffer Associate Professor of Chemistry Theoretical and Computational Chemistry at Penn State to see interactive graphs for these potential functions.


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Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.