Qmmm link atoms

link_atoms <(hydrogen||halogen) default halogen>

This directive controls the treatment of bonds crossing the boundary between quantum and classical regions. The use of hydrogen keyword will trigger truncation of such bonds with hydrogen link atoms. The position of the hydrogen atom will be calculated from the coordinates of the quantum and classical atom of the truncated bond using the following expression

\[\mathbf{R}_{hlink} = (1-g)\mathbf{R}_{quant} + g*\mathbf{R}_{class}\]

where g is the scale factor set at 0.709

Setting link_atoms to halogen will result in the modification of the quantum atom of the truncated bond to the fluoride atom. This fluoride atom will typically carry an effective core potential (ECP) basis set as specified in link_ecp directive.