Molecular dynamics simulation

Question

[toyan.j.p]

Hi,

I am trying to understand MD simulation and am a novice. How is RMSD vs time plot of wildtype and mutant proteins interpreted? What is the relative position of wildtype trajectory in terms of mutants (which are say prospective candidates for unfolding). And why is PCA analysis done on MD trajectories? Would it help in deciphering potential candidate mutants for unfolding of protein?

Thanks in advance for any help

Regards Toyanji Joseph