# Rmsd calculation using gmx rms
**URL:** https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566
**Category:** User discussions
**Created:** [February 17, 2025, 6:17am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566 "2025-02-17T06:17:04Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@dulal](https://gromacs.bioexcel.eu/u/dulal)
#### Post date: [February 17, 2025, 6:17am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566/1 "2025-02-17T06:17:04Z")
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Dear Experts,
I am trying to calculate protein backbone rmsd. But I got thr following error message.
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 50896 atoms. The longest distance involved in such interactions
is 6.694 nm which is above half the box length. This molecule type consists of
multiple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
Thanking you in advance
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### Author:  [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)
#### Post date: [February 18, 2025, 4:56am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566/2 "2025-02-18T04:56:37Z")
Maybe you should use these commands to make sure there are no shifts over the periodic boundary conditions: First - gmx trjconv -s your\_tpr.tpr -f your\_traj.xtc -o whole.xtc -pbc mol
and then next - gmx trjconv -s your\_tpr.tpr -f whole.xtc -o centered.xtc -center -pbc mol
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### Author:  [@dulal](https://gromacs.bioexcel.eu/u/dulal)
#### Post date: [February 18, 2025, 5:59am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566/3 "2025-02-18T05:59:12Z")
Thank you for your response.
But when I type the command
gmx trjconv -s …/prod1.tpr -f …/40.xtc -o whole.xtc -pbc mol
I got the same error message.
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 50896 atoms. The longest distance involved in such interactions
is 6.694 nm which is above half the box length. This molecule type consists of
multiple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size
---
### Author:  [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)
#### Post date: [February 18, 2025, 8:25am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566/4 "2025-02-18T08:25:09Z")
Did you try increasing the box size ?
is it a cubic solvation box that you have used?
---
### Author:  [@dulal](https://gromacs.bioexcel.eu/u/dulal)
#### Post date: [February 18, 2025, 10:49am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-using-gmx-rms/11566/5 "2025-02-18T10:49:24Z")
Thank you for your reply.
Yes, it is a cubic salvation box (8.0 nm).
I have already perform 40 ns production run.
Then I have to increase box size.
I type the following command.
gmx trjconv -s …/prod1.tpr -f …/40.xtc -o test.xtc -box 20.0 20.0 20.0 -pbc mol -center
gmx rms -s …/prod1.tpr -f test.xtc -o rmsd.xvg -pbc no
this works.
is it correct?