How to view the conformation change in protein after 50 ns MD simulations?
You can load the trajectory into VMD, and then do an alignment with the alpha carbon atoms of the protein (VMD--Extensions--Analysis--RMSD Trajectory Tool). After that you can view the confrontational change by watching the trajectory.
You can load it in the Discovery studio software.
I use Discovery Studio Visualizer v17.2.0.16349. How to load it? Please let me know.
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