differently depending on the treatment of the aromatic residues.
Parameters for the virtual site constructions for the hydrogen atoms are
-inferred from the force field parameters ({\em vis}. bond lengths and
+inferred from the force-field parameters ({\em vis}. bond lengths and
angles) directly by {\tt \normindex{grompp}} while processing the
topology file. The constructions for the aromatic residues are based
on the bond lengths and angles for the geometry as described in the
electrons and the MM atoms. The total electrostatic interaction of the
QM nuclei with the MM atoms is given by the second double sum. Bonded
interactions between QM and MM atoms are described at the MM level by
-the appropriate force field terms. Chemical bonds that connect the two
+the appropriate force-field terms. Chemical bonds that connect the two
subsystems are capped by a hydrogen atom to complete the valence of
the QM region. The force on this atom, which is present in the QM
region only, is distributed over the two atoms of the bond. The cap
At the bond that connects the QM and MM subsystems, a link atoms is
introduced. In {\gromacs} the link atom has special atomtype, called
LA. This atomtype is treated as a hydrogen atom in the QM calculation,
-and as a virtual site in the force field calculation. The link atoms, if
+and as a virtual site in the force-field calculation. The link atoms, if
any, are part of the system, but have no interaction with any other
atom, except that the QM force working on it is distributed over the
two atoms of the bond. In the topology, the link atom (LA), therefore,