# RMSD graph indicated that the protein-protein complex is not stable

**URL:** <https://gromacs.bioexcel.eu/t/rmsd-graph-indicated-that-the-protein-protein-complex-is-not-stable/9114>\
**Category:** User discussions\
**Created:** [May 9, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/rmsd-graph-indicated-that-the-protein-protein-complex-is-not-stable/9114 "2024-05-09T07:09:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![nurarshad](https://avatars.discourse-cdn.com/v4/letter/n/ed655f/32.png) [@nurarshad](https://gromacs.bioexcel.eu/u/nurarshad)\
**Post date:** [May 9, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/rmsd-graph-indicated-that-the-protein-protein-complex-is-not-stable/9114/1 "2024-05-09T07:09:31Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Hi all, I have seen others published RMSD graph on their simulations and what I can interpret is that the RMSD graph should have mild fluctuations to indicate that the protein is stable.

However, after analysing the RMSD graph from my simulations, I guessed I could interpret that my protein-protein complex is not stable. So, does this means the protein-protein complex cannot happen in real-life situations?

 ![Screenshot 2024-05-09 at 11.27.38 AM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/f/f3c6e36702c4d40e382c7e657f0479917293cf9c.png)  
 ![rmsf-kwt2-fixed-nojump](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8eacf8ce530bb42af7cfcc273dcab98a1e78f478.png)

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [May 23, 2024, 3:10pm UTC](https://gromacs.bioexcel.eu/t/rmsd-graph-indicated-that-the-protein-protein-complex-is-not-stable/9114/2 "2024-05-23T15:10:13Z")

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All you can really interpret from a large RMSD is that the conformation of the protein differs from its starting conformation, not necessarily that such changes are unrealistic. I would suggest visualizing the protein to see what’s causing these fluctuations

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**Author:** ![asif2](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@asif2](https://gromacs.bioexcel.eu/u/asif2)\
**Post date:** [July 1, 2024, 5:01am UTC](https://gromacs.bioexcel.eu/t/rmsd-graph-indicated-that-the-protein-protein-complex-is-not-stable/9114/3 "2024-07-01T05:01:22Z")

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Hey nurarshad

The RMSD graph seems unstable, but you can make things work.  
You can attempt another MD simulation, but this time, consider a longer NPT equilibration period. Once equilibrated, verify the pressure constant of the resulting complex.

> gmx energy -f npt -o pressure.xvg

Positive pressure supports less RMSD fluctuation; if things are still not working, you need to re-parametrize the ligand with a different force field or go with a longer run so that after 150 ns you can expect a stable trajectory.