energy_data.contact_shell — nonbond distance cutoff

This defines the maximal distance (in angstroms) 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. The default value is 4.0 Å.

If undefined ($-999$ ), the distance is the maximum of:

• If energy_data.dynamic_sphere is True, 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).

• If energy_data.dynamic_lennard is True, energy_data.lennard_jones_switch[1].

• If energy_data.dynamic_coulomb is True, energy_data.coulomb_switch[1].

• The maximum cutoff distance requested by any user-defined energy term, if the scaling factor of that term is non-zero (see Section 7.1.3).

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 A.3.1.