[gmx-users] sudden jumps in RMSD etc.

Yun Shi yunshi09 at gmail.com
Thu Jan 19 21:55:46 CET 2012

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,

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