[gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

[Quin K]

Hi

During RMSD analysis of protein ligand complex I got the following graph.
RMSD of how much the ligand position has varied relative to the protein is
given in the graph (Please see the link below).

https://drive.google.com/file/d/1rvkHYisjmjFDvN6Lldo5Gejz7nJKEKnl/view?usp=sharing

I noted that there is a lot of variation in the graph. Is this normal?
Should I continue with the simulation for 100 ns? Or should I redo the
simulation all over?

Thank you
Regards