You’re applying fix nvt to all atoms, and some appear
to be fixed. I don’t know which atoms you are including
when you say the output Temp is 400. Both of these
are issues you have to be careful about if you want
to thermostat and monitor the temperature accurately.
I recommend that unless you have the data/arguments to prove that a given feature in Lammps doesn’t work, next time try for email subject: “Problems with setting the temp with fix nvt in Lammps”, or “My brain doesn’t work and thus I cannot understand why the temp from fix nvt is not the one I expect…” , etc. In your case chances are the fix nvt is working just fine and it is you are the one who doesn’t know how to use it.