3. Molecular mechanics

3.1 Definition

Molecular mechanics is the direct application of a force field to a given system, with the principal aim of obtaining its energy. So, for a molecule drawn on a screen or represented by its internal or Cartesian coordinate matrix, molecular mechanics will provide us with an energy. However, this energy does not correspond to the molecule's minimum energy. Why should it? There's no reason why we should draw the conformation of the molecule, or the system, in its most stable state. It is therefore imperative to optimize its structure so that it conforms as closely as possible to reality, or at least to the "reality" expressed by the force field. We therefore need to find a way of obtaining the molecule in its energetically stable state. This is achieved by various means,...