The 'link bonds' are those covalent bonds that cross the QM-MM boundary in the full QM/MM system. A link bond involves one atom that belongs to the MM region and one from the QM region, see Figure 1-1a. The 'capping atoms' (sometimes termed dummy atoms) refer to the atoms that are used to cap the valence in the model QM system. Capping atoms are not part of the full system. The 'capping bond' is the covalent bond in the QM model system that corresponds to the link bond in the real system. The terms capping atom or capping bond only refer to the model QM system, whereas the term LINK only refers to bonds or atoms in the real system.
