If I want to use gmx trjconv to recenter the protein in xtc file, the reference 
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the 
first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use 
md.tpr as reference for md.xtc, I will have to recenter it after every step of 
em, nvt, npt
Kind Regards,Ahmed 

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