Understanding the Results

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 .