Minimization does not respect SHAKE bond distances - so you wouldn't
want to start a run with SHAKE with bond distances that are very far
off. Maybe you should run dynamics for a few steps, then turn on SHAKE.
Another comment on minimization with SHAKE. Since mininize
in LAMMPS does not enforce the SHAKE bond distances you need
to do the minimize with bonds in place that will keep the bond distances
close to the SHAKE fixed distances.