Ultimately the validity of the results depends on the accuracy of the
potentials and the appropriateness of the calculation. Molecular mechanics is not a
thermodynamic calculation or average over an ensemble.
Two commands in AMMP can be used to analyze the results.
Analyze low_atom high_atom ; generates detailed listings of the errors in the
currently selected potentials. Atoms which are inactive usually are not shown.
Monitor ; calculates the energies with the currently selected potentials.
Monitor also updates the forces. The individual forces on atom j can be found
with the variables j.fx,j.fy,j.fz .