# Unstable RMSD Fluctuations in Protein Simulation: Potential Issues?

**URL:** <https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412>\
**Category:** User discussions\
**Created:** [October 25, 2024, 3:24am UTC](https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412 "2024-10-25T03:24:59Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [October 25, 2024, 3:24am UTC](https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412/1 "2024-10-25T03:24:59Z")

</div>

GROMACS version: gromacs-2022.2

"Hello everyone,

I’m seeking some guidance on interpreting the attached RMSD plot of a molecular dynamics simulation for a protein backbone after fitting into the backbone itself. The plot shows fluctuations in RMSD over a 200 ns simulation, with notable instability and large deviations starting around 80 ns (Uploading the plot along). RMSD values range between 1 nm and 7 nm, with periods of high variability.

I wonder if this behavior is normal for such a simulation or if it could indicate a technical issue with the setup, simulation parameters, or system stability. Any insights on possible causes and suggestions for improving the analysis would be greatly appreciated.

Thank you!"

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/044b769702b0998f9943a8948de40749ca664bfa.png)

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 25, 2024, 6:40am UTC](https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412/2 "2024-10-25T06:40:52Z")

</div>

It looks like it’s just a matter of periodic boundary conditions. Have you tried `gmx trjconv -pbc nojump` before analysing the trajectory?

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 25, 2024, 6:42am UTC](https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412/3 "2024-10-25T06:42:41Z")

</div>

You might need to first do a conversion with `gmx trjconv -pbc mol` before `gmx trjconv -pbc nojump`.

---

<div class="post-metadata">

**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [October 27, 2024, 1:50pm UTC](https://gromacs.bioexcel.eu/t/unstable-rmsd-fluctuations-in-protein-simulation-potential-issues/10412/4 "2024-10-27T13:50:31Z")

</div>

Will Definitely try this. Thank you.  
I have done - gmx trjconv -pbc mol, will try the nojump command.