The RMSD trajectory for bare protein nd complex almost identical. So when i plot it i cannot diffrentiate it.
You can do one thing....
try to take snapshots at different time points of trajectory to verify that the protein is intact or not within the protein.....
Sometimes if the ligand is out of the simulation box.... the trajectory will be as same as bare protein.....
Regards
when i play the simulation, the ligand is in intact within the protein, also i don't see the simulation box. what shall i do then?
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