iii) refining the dihedrals selection and related atom quadruplets by defining each torsion according to the bond order of the inner atoms. That is, grouping the coordinates in stiff, (φ ) or flexible (δ ) coordinates according to equations ( ) and ( ) and automatically assigning them to either harmonic or periodic potential model functions, respectively. iv) automatically identifying the internal distances r so f t . JOYCE3.0 provides a list of all atom pairs that are found to be more than three bonds apart, from which the user can select only the pairs necessary to represent specific intramolecular non-bonded interactions, such as those involved in intramolecular HBs, or to avoid 'bad contacts', which can occur in very flexible molecules, between atoms that are far apart.