PENA — Activate penalty function on the molecule’s moments of inertia.
During the simulated annealing process, molecular systems are prone to dissociate due to the random nature of the forces driving the annealing. Dissociation poses serious problems for simulated annealing because there is no force to indicate how to recombine the fragments. The PENA penalty function was developed to prevent this by applying a penalty to systems that are moving toward dissociation. PENA operates by computing the moment of inertia of a given conformation (treating each of the masses as one) and applying a penalty of this moment of inertia exceeds a certain threshold. Since the moment of inertia is strongly system dependent, PENA penalty threshold is defined relative to the moment of inertia of the initial configuration. That is, the PENA penalty will be applied to a configuration if its moment of inertia exceeds n.n times the moment of inertia of the input molecule. The value of n.n must be greater than 1.0 and generally should be in the range 1.1 to 3.0.
Note that this penalty is also active in the course of quenching. During the quenching stage, the output file reports “RATIO INERTIA / BORDER,” for each remaining configuration. If this ratio exceeds 1.0, then that conformation is penalized and the magnitude of the penalty is reported on the next line as “PENALTY FUNCTION (KCAL).”
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