Compare snapshots along the trajectory and look at the residue rmsd along to protein sequence to see whether a specific region of the protein becomes more flexible.

For some proteins, e.g. some kinases, a regulatory loop binds into the substrate binding site of the apo protein to inhibit its activity. Phosphorylation of regulatory residues in the loop prevent this interaction with the substrate binding site, making the loop more flexible and allowing the substrate to bind.

Annemarie Honegger Thank you for your answer and yes i am working on kinase protein. So, how will i consider which one is more stable when compared between the apo and the protein ligand complex (if the protein ligand rmsd value is higher than the apo)?

RMSD of complex and the apo protein can well be different because after binding with the ligand protein might undergo some confirmational changes. May be ligand binding results in more movement in some part of protein leading to its higher RMSD value compared to Apo protein.