Dear Vinayak
Are you still running with hybrid functionals?
If yes, I would suggest to switch to a GGA functional until the structure is equilibrated at the desired conditions.
Finer calculation of the electronic properties by means of higher level theory, e.g., hybrids, are significantly more expensive and should be used only when they really needed.
The thermostat might need substantially more than 500 fs to bring the system to the desired temperature.
Playing with the parameter of the thermostat might help to speed this process up.
During the equilibration part of the simulation, you can also apply a temperature tolerance, which will force the temperature to remain within a certain range by rescaling the velocities.
The part of the simulation where such a velocity rescaling is active cannot not be considered a proper sampling of the ensemble.
Regards
Marcella