Please reply to the list, not to me.
The problem with velocity scale is that it knows nothing
about rigid bodies. If you just change the velocity of an atom
in a rigid body, it will not persist, b/c the rigid body constraints
will do their own thing. Instead you need to thermostat
the rigid body. Several of the fix rigid commands have options
for this, langevin or Nose/Hoover. They act on the
3 translational and 3 rotational DOF for the body itself.
Steve