# RMSD with trjconv and -pbc no
**URL:** https://gromacs.bioexcel.eu/t/rmsd-with-trjconv-and-pbc-no/7137
**Category:** User discussions
**Tags:** analysis-tools
**Created:** [September 6, 2023, 1:28pm UTC](https://gromacs.bioexcel.eu/t/rmsd-with-trjconv-and-pbc-no/7137 "2023-09-06T13:28:35Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@amaligg](https://gromacs.bioexcel.eu/u/amaligg)
#### Post date: [September 6, 2023, 1:28pm UTC](https://gromacs.bioexcel.eu/t/rmsd-with-trjconv-and-pbc-no/7137/1 "2023-09-06T13:28:35Z")
Hi All,
My system contains polymers and water. I want to calculate the RMSD of polymer chains after the simulation. For this purpose, I used the following commands.
A i) gmx trjconv -f md01.tpr -f md01.xtc -o md01\_nopbc.xtc -pbc nojump
ii) gmx rms -s md01.tpr -f md01\_nopbc.xtc -o rmsd\_chainA.xvg -n index.ndx -tu ns
Also, I tried with the following command separately (didn’t do any trjconv).
B) gmx rms -s md01.tpr -f md01.xtc -o rmsd\_ChainA\_2.xvg -n index.ndx -tu ns -pbc no
I removed the pbc conditions in A (using trjconv) and B (using -pbc no) methods (as per my understanding, please correct me if I am wrong). Yet, I got two different graphs for RMSD.
Appreciate your help in understanding this.
Thank you.
Best regards
Amali
---
### Author:  [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)
#### Post date: [October 3, 2023, 7:58am UTC](https://gromacs.bioexcel.eu/t/rmsd-with-trjconv-and-pbc-no/7137/2 "2023-10-03T07:58:42Z")
`gmx rms` with `-pbc no` means that you are not taking periodic boundary conditions into account. That would probably work after having run your `trjconv` command, but not without it.
I think (but cannot promise) that you would get similar results with:
```auto
A i) gmx trjconv -f md01.tpr -f md01.xtc -o md01_nopbc.xtc -pbc nojump
ii) gmx rms -s md01.tpr -f md01_nopbc.xtc -o rmsd_chainA.xvg -n index.ndx -tu ns -pbc no
```
and
```auto
B) gmx rms -s md01.tpr -f md01.xtc -o rmsd_ChainA_2.xvg -n index.ndx -tu ns
```