Abstract
A new treatment is presented for calculating the molecular mechanics intramolecular atom–atom Coulomb potential energy. It is shown that the standard method of only including charge pairs in the 1,4 and higher positions is unphysical, and leads to erratic electrostatic relative energies especially when the atomic charges are allowed to vary during a simulation. The problem is removed with the new scheme that partially also includes 1,2 and 1,3 interactions as needed to balance the charges in the 1,4 positions. A few simple molecules that involve conformation-dependent charges are used to illustrate the advantages of the new procedure.
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