Temperature is base on the average kinetic motion of all atoms

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Sorry for this silly question , I am still high school student . I know that temperature is base on the average kinetic motion of all atoms. But kinetic motion is not absolute so in what case should we use this formula: v= [tex]\sqrt{\frac{3RT}{\mu}}[/tex] . Should it be the velocity in respect to the center of mass? In that case , two objects have the same average velocity may have different temperature like that when we open a box fill with vacuum and close it fast enough when the temperature inside that box is different from outside because the air only go in the box in one way . Thank you for reading my question .
 

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