# The inconsistent shifts in the RMSD graphs

**URL:** <https://gromacs.bioexcel.eu/t/the-inconsistent-shifts-in-the-rmsd-graphs/11819>\
**Category:** User discussions\
**Created:** [March 27, 2025, 4:19am UTC](https://gromacs.bioexcel.eu/t/the-inconsistent-shifts-in-the-rmsd-graphs/11819 "2025-03-27T04:19:46Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [March 27, 2025, 4:19am UTC](https://gromacs.bioexcel.eu/t/the-inconsistent-shifts-in-the-rmsd-graphs/11819/1 "2025-03-27T04:19:46Z")

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The RMSD generation in gromacs is providing inconsistent shifts over the period of simulation. How can this problem be fixed? Attaching an RMSD graph for reference. Please help me out.

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9e1a01c7b187ef0c7b01f58d50afdc1332c5841c.png)

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**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [March 27, 2025, 9:09am UTC](https://gromacs.bioexcel.eu/t/the-inconsistent-shifts-in-the-rmsd-graphs/11819/2 "2025-03-27T09:09:10Z")

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You have to clean up the trajectory over which you are computing the RMSD. This is usually done with `gmx trjconv` and specific `-pbc` flags such as `whole` or `nojump` etc. Take a look at the [manual](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html).