Hi all, I am doing duplicate MD simulations with a protein-ligand system.
After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then -fit progressive on protein atoms, which again did not completely eliminate those jumps in protein atom RMSDs. I wonder if I have not used the right option? Thanks for any advice, Yun
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