energy_data.contact_shell -- nonbond distance cutoff

Description:

This defines the maximal distance between atoms that flags a non-bonded atom pair. Such pairs are stored in the list of non-bonded atom pairs. Only those non-bonded pairs that are sufficiently close to each other will result in an actual non-bonded restraint.

If undefined ($-999$), the default value is the maximum of the three possibilities: twice the radius of the largest atom multiplied by energy_data.radii_factor (in the case of the all non-hydrogen atoms model, this is 3.2 Å); energy_data.lennard_jones_switch[1]; or energy_data.coulomb_switch[1]. Only those values of the three possibilities are compared that have the corresponding energy_data.dynamic_sphere, energy_data.dynamic_lennard, or energy_data.dynamic_coulomb set to True.

The best value for energy_data.contact_shell must be found in combination with energy_data.update_dynamic (see also below). Good values are 4Å for energy_data.contact_shell and 0.39Å for energy_data.update_dynamic when no Lennard-Jones and Coulomb terms are used; if energy_data.contact_shell is larger, there would be many pairs in the non-bonded pairs list which would slow down the evaluation of the molecular pdf. If it is too small, however, the increased frequency of the pair list recalculation may slow down the optimization.

This distance is also used for the calculation of atomic density; see section 6.3.1.