question regarding rmsd

From: Dhiraj Srivastava (
Date: Tue Oct 04 2016 - 16:07:43 CDT

   I am trying to do MD simulation on a protein with and without ligand.
when I did rmsd plot, I found that apo protein is behaving fine (red) but
ligand bound form (black) is taking relatively longer time to equilibrate
and showing quite a bit of fluctuation in rmsd. is the fluctuation in rmsd
value for ligand bound protein is acceptable or is there anything wrong?
How can I fix it?


[image: Inline image 3]


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