How to get rid of the jumps in rmsd calculation in gromacs??

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Daryna Smyrnova

Use trjconv tool to get rid of jumps in the trajectory. First use

-pbc nojump and then fit the trajectory to the first frame with

-fit rot+trans.

Malsha Jayasinghe

Thank you very much for your reply. But both methods didn't work. How to visualize the system?? may be the system has crashed.

Thank you very much i'll try!