# RMSD calculation error

**URL:** <https://gromacs.bioexcel.eu/t/rmsd-calculation-error/7792>\
**Category:** User discussions\
**Tags:** mdrun, gmx-trjconv, pmx\
**Created:** [December 5, 2023, 3:30am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-error/7792 "2023-12-05T03:30:31Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![nhina](https://avatars.discourse-cdn.com/v4/letter/n/46a35a/32.png) [@nhina](https://gromacs.bioexcel.eu/u/nhina)\
**Post date:** [December 5, 2023, 3:30am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-error/7792/1 "2023-12-05T03:30:31Z")

</div>

GROMACS version: 2019  
GROMACS modification: Yes/No  
Hi All,

My system contains protein, ligand and nowater. I want to calculate RMSD after simulation and i have used commands.

gmx trjconv -s md\_1.tpr -f md\_1.xtc -o traj\_1.xtc -pbc nojump  
gmx rms -s md\_1.tpr -f traj\_1.xtc -o rmsd\_noH\_1.xvg -n Pro\_MOL\_noH.ndx -tu ns

After i run commands then program warms an error like that

 ![rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8138f9b21a04e3464816a861844efe750c31c763.jpeg)

Appreciate your help in fixing this.

Thank you.

Best regards  
Hang NT Nguyen

---

<div class="post-metadata">

**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\
**Post date:** [December 6, 2023, 4:41pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-error/7792/2 "2023-12-06T16:41:20Z")

</div>

what is included in the index (.ndx\*) file?Try to calculate RMSD of only protein (or C-alpha atoms) and save the first frame of the trajectory as your reference.