# RMSD calculation

**URL:** <https://gromacs.bioexcel.eu/t/rmsd-calculation/1907>\
**Category:** User discussions\
**Created:** [April 6, 2021, 3:51pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation/1907 "2021-04-06T15:51:57Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![aysebercinb](https://avatars.discourse-cdn.com/v4/letter/a/5daacb/32.png) [@aysebercinb](https://gromacs.bioexcel.eu/u/aysebercinb)\
**Post date:** [April 6, 2021, 3:51pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation/1907/1 "2021-04-06T15:51:57Z")

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GROMACS version: 2020.4

Hi,

I am working with a complex includes protein, DNA and small molecule. After my 500 ns simulation, I used to want to calculate RMSD changes of this system during the simulation. I generated an index file with: gmx make\_ndx -f complex.gro. And I gave an index to Protein+DNA+SmallMolecule. For RMSD calculation, I selected this group twice, however my RMSD values above 3.5 nm. If I choose Backbone or Protein groups twice, RMSD values are decrasing to ~0.2 nm.  
I calculated each group seperately (Protein, DNA and Small Molecule) and the values are ~0.2 nm.  
Is the problem about making index file or generating new group?

Thanks in advance

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 6, 2021, 6:26pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation/1907/2 "2021-04-06T18:26:41Z")

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Probably you have pieces of your system jumping across periodic boundaries so the complex isn’t always together. Re-image with `trjconv` and you should be able to compute the RMSD of the whole complex.

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**Author:** ![aysebercinb](https://avatars.discourse-cdn.com/v4/letter/a/5daacb/32.png) [@aysebercinb](https://gromacs.bioexcel.eu/u/aysebercinb)\
**Post date:** [April 6, 2021, 6:58pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation/1907/3 "2021-04-06T18:58:51Z")

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Thank you for your answer.  
However I applied image correction to my system and I am sure the system is not jumping. May my system has any other problem?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 8, 2021, 1:01pm UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation/1907/4 "2021-04-08T13:01:34Z")

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Without seeing your exact commands, selections, and the plots themselves, there’s not really much to go on.