# RMSF values are different for same residues, same trajectory

**URL:** <https://gromacs.bioexcel.eu/t/rmsf-values-are-different-for-same-residues-same-trajectory/12210>\
**Category:** User discussions\
**Created:** [June 6, 2025, 12:27pm UTC](https://gromacs.bioexcel.eu/t/rmsf-values-are-different-for-same-residues-same-trajectory/12210 "2025-06-06T12:27:16Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Uddipta](https://avatars.discourse-cdn.com/v4/letter/u/a8b319/32.png) [@Uddipta](https://gromacs.bioexcel.eu/u/Uddipta)\
**Post date:** [June 6, 2025, 12:27pm UTC](https://gromacs.bioexcel.eu/t/rmsf-values-are-different-for-same-residues-same-trajectory/12210/1 "2025-06-06T12:27:16Z")

</div>

GROMACS version: 2022  
GROMACS modification: No

I have calculated the RMSF values of a **whole protein**.  
Later I created a **new index** file, selecting a few specific residues, and again calculated the RMSF on that index.  
In both cases, same trajectory and tpr file were used.  
But **the RMSF values of the same residues are found to be different in both cases**.  
( I used entire residues with hydrogens in both cases)