Dear Antonis
It might be due to how you treat the periodicity of the QM part.
I noticed that in the QMMM subsection the cell is much smaller, the periodicity is set xyz, but the multiples for de-coupling and recoupling are set to off.
This looks like a strange choice of settings.
Did you try a to run MM and then restart from an equilibrated MM run?
The MM cell is rather large with respect to the size of the systems. Moreover there are fixed atom constraints that also are pretty unusual when simulating water.
Regards
Marcella