For a QM/MM calculation a subset of atoms are selected from the classical restart and then for this QM part an isolated system (SYMMETRY 0) calculation is performed. The supercell size has to follow the requirements of the various Poisson solvers, as listed in the hints section (9.4).
If not otherwise specified, the QM system (atoms and wavefunction) is always re-centered in the given supercell (the current offset of the QM cell is recorded in the http MM_CELL_TRANS).
The quantum atoms are specified in the &ATOMS section similar to normal CPMD calculations. Instead of explicit coordinates one has to provide the atom index as given in the Gromos topology and coordinates https.