[Info] Significance of minimum-energy structure from a forcefield-based simulation


The following is an excerpt from some very old documentation but I have always thought that it was quite useful for understanding minimization and the minimized molecule's calculated energy.


Calculated energy is relative

In dealing with macromolecular optimization calculations, it is important to keep in mind the theoretical significance of the minimum-energy structure and its calculated energy. For all forcefields used in calculations of this type, the energy zero is arbitrary, and therefore, the total potential energy of different models cannot be compared directly. However, it is meaningful to make comparisons of energies calculated for different configurations of chemically identical models. In principle, the calculated energy of a fully minimized structure is the classical enthalpy at absolute zero, ignoring quantum effects (in particular the zero-point vibrational motion). For a model that is sufficiently small that its normal modes can be calculated, quantum corrections for zero-point energy and the free energy at higher temperatures can be taken into account.