If you would also like to know if your protein is conformationally stable after the equilibration you have to calculate the RMSD of the protein backbone.
This will give you an idea of the stability of the protein. If the RMSD is still increasing at the end of the run, it means your protein is still searching for a lower energy state, and thus is not yet equilibrated!
RMSD.tcl can found at [ Ссылка ]
