# How does gromacs calculate RMSD for proteins?

**URL:** <https://gromacs.bioexcel.eu/t/how-does-gromacs-calculate-rmsd-for-proteins/10010>\
**Category:** User discussions\
**Created:** [August 27, 2024, 2:14pm UTC](https://gromacs.bioexcel.eu/t/how-does-gromacs-calculate-rmsd-for-proteins/10010 "2024-08-27T14:14:05Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Bijaya](https://avatars.discourse-cdn.com/v4/letter/b/bcef8e/32.png) [@Bijaya](https://gromacs.bioexcel.eu/u/Bijaya)\
**Post date:** [August 27, 2024, 2:14pm UTC](https://gromacs.bioexcel.eu/t/how-does-gromacs-calculate-rmsd-for-proteins/10010/1 "2024-08-27T14:14:05Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
Dear All,  
I have come across something strange while doing RMSD calculation.  
I calculated the RMSD of a mutated protein using the .tpr file generated from Wild type and it does the calculation without any error. Both the systems have different number of atoms and I was anticipating an error, but that didnt happen. Infact, I tried the calculation using totally unrelated .tpr from a different protein and yet it prints some values.  
Now I’m totally confused about whats happening. I tried the calculation using two versions of gromacs:2020.2 and 2022 as well.  
Can anyone explain what might have gone wrong here ? Or am I making some mistake in understanding.  
Thanks and Regards