# Rmsf according to referans gro files

**URL:** <https://gromacs.bioexcel.eu/t/rmsf-according-to-referans-gro-files/7327>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [October 4, 2023, 6:09am UTC](https://gromacs.bioexcel.eu/t/rmsf-according-to-referans-gro-files/7327 "2023-10-04T06:09:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ozge](https://avatars.discourse-cdn.com/v4/letter/o/e47774/32.png) [@ozge](https://gromacs.bioexcel.eu/u/ozge)\
**Post date:** [October 4, 2023, 6:09am UTC](https://gromacs.bioexcel.eu/t/rmsf-according-to-referans-gro-files/7327/1 "2023-10-04T06:09:49Z")

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GROMACS version: VERSION 5.1.4  
GROMACS modification: No  
I have ref\_open and ref\_closed files for MurD protein. I want to calculate rmsf of MurD\_closed.gro with average. I thought gmx-rmsf command calculates average coordinates in the trajectory. But I got the different rmsf values when I used the different referans files. I used this codes :

- gmx\_mpi rmsf -f MurD\_closed.gro -s ref\_closed.gro -o rmsf\_closed\_refclosed.xvg
- gmx\_mpi rmsf -f MurD\_closed.gro -s ref\_open.gro -o rmsf\_closed\_refopen.xvg  
I tried -res and -fit flag but there is no difference between the values. Can you help me? Does anyone have any ideas on this subject? How can I calculate based on average? Thank you :)

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 4, 2023, 1:16pm UTC](https://gromacs.bioexcel.eu/t/rmsf-according-to-referans-gro-files/7327/2 "2023-10-04T13:16:02Z")

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RMSF is computed relative to the average coordinates over the trajectory. The reference structure in `-s` is used for least-squares fitting, if specified (which is the default behavior).