I'm a PhD student and I'm using modeller version 9. I'd very glad if you
could explain to me which is the solvation model used by modeller in the
various steps (in particular in the simulated annealing refinement
procedure, CG_minimization, MD etc.)
No solvation model is used. The effect of solvation, like
electrostatics, is assumed to be encoded in the structure of your
template(s), and thus in the distance restraints derived from those
templates.
and the temperatures at which SA is
carried out in the high optimization level procedure.
Look at the Python functions defined in
modlib/modeller/automodel/refine.py under your Modeller installation
directory. They define the temperatures and other parameters for the SA
dynamics runs.