Gmx rms command

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GROMACS version:
GROMACS modification: Yes/No

Hello all, I have a protein ligand complex trajectory, and I want to calculate the ligand RMSD after aligning the protein structure. My idea is that if I calculate ligand rmsd after fitting protein first, then if the ligand would be moving away then it would be reflected in the ligand RMSD. I am using gmx rms command, and after submitting the command it asks me

  1. Select group for least squares fit
    then 2. Select a group: Select group for RMSD calculation
    If I select protein group in the first option, and then ligand group in the second option, then will it serve my purpose?
    The ligand RMSD I am getting such a way are not looking like what I want.
    What mistake I am doing, and what can be possible way to get what I want?
    Any help would be highly appreciated.
    Thanks.
    Rakesh Srivastava