Dear Lina, could you express these commands clearly? I am a new user!
editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_ box.gro -center x/2 y/2 z/2 -box x y z genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o they_are_in_the_same_box_now.gro -p topol.top
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