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.