# Gmx rms command

**URL:** <https://gromacs.bioexcel.eu/t/gmx-rms-command/6427>\
**Category:** User discussions\
**Created:** [May 17, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-command/6427 "2023-05-17T14:04:37Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![rakesh26](https://avatars.discourse-cdn.com/v4/letter/r/cdc98d/32.png) [@rakesh26](https://gromacs.bioexcel.eu/u/rakesh26)\
**Post date:** [May 17, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-command/6427/1 "2023-05-17T14:04:37Z")

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GROMACS version:  
GROMACS modification: Yes/No

Hello all, I have a protein ligand complex trajectory, and I want to calculate the ligand RMSD after aligning the protein structure. My idea is that if I calculate ligand rmsd after fitting protein first, then if the ligand would be moving away then it would be reflected in the ligand RMSD. I am using gmx rms command, and after submitting the command it asks me

1. Select group for least squares fit  
then 2. Select a group: Select group for RMSD calculation  
If I select protein group in the first option, and then ligand group in the second option, then will it serve my purpose?  
The ligand RMSD I am getting such a way are not looking like what I want.  
What mistake I am doing, and what can be possible way to get what I want?  
Any help would be highly appreciated.  
Thanks.  
Rakesh Srivastava