This specifies the number of atoms that must be selected in each nonbonded pair, in order for the energy term to be calculated. Thus, when only a subset of all atoms is used in energy evaluation, this variable controls the interaction between the picked atoms and the rest of the system. When it is 2, the non-bonded pairs will contain only selected atoms. This means that the optimized atoms will not ``feel'' the rest of the protein through the non-bonded terms at all.
If energy_data.nonbonded_sel_atoms is 1 (the default), only one of the atoms in the non-bonded pair has to be a selected atom. This means that the selected region feels the rest of the system through the non-bonded terms, at the expense of longer CPU times.
See Section 2.2.6 for an example.
When all atoms are selected, this variable has no effect.