Hi Manissri,
When you are about to find the PM or the loop gain of a feedback system, you have to run the AC analysis over freq. So, all your input of your opamp should be given dc value. If you ground the input to opamp, then your circuit is not operating and all the dc point of the subsequent stages is not in actual dc operating condition. Thus giving 2.5V at your opamp is fine to measure your loop gain and PM. Pls see the attach file for middle brook measurement.
Thanks,
Suria