energy_data.update_dynamic — nonbond recalculation threshold

This sets the cumulative maximal atomic shift (in angstroms) during optimization that triggers recalculation of the list of atom-atom non-bonded pairs. It should be set in combination with energy_data.contact_shell. The default value is 0.39 Å.

For soft-sphere overlap, to be absolutely sure that no unaccounted contacts occur, energy_data.update_dynamic has to be equal to (energy_data.contact_shell - maximal_overlap_distance) / 2. maximal_overlap_distance is equal to the diameter of the largest atom in the model; it is 3.2 Å in the case of the all non-hydrogen atoms model. This distance is the energy_data.contact_shell value if a default is requested. Factor 2 comes from the fact that the moves of both atoms can reduce the distance between them.