energy_data.nonbonded_sel_atoms — control interaction with picked atoms

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.