# How to get a continous rmsf graph for mutiple chains?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-get-a-continous-rmsf-graph-for-mutiple-chains/2504>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [July 13, 2021, 1:58pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-a-continous-rmsf-graph-for-mutiple-chains/2504 "2021-07-13T13:58:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![explodedpt](https://avatars.discourse-cdn.com/v4/letter/e/8baadc/32.png) [@explodedpt](https://gromacs.bioexcel.eu/u/explodedpt)\
**Post date:** [July 13, 2021, 1:58pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-a-continous-rmsf-graph-for-mutiple-chains/2504/1 "2021-07-13T13:58:18Z")

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Hi all.

I have just finished my first MD.  
Then I did rmsf analysis as follows  
$ gmx rmsf -s md\_0\_10.tpr -f md\_fit\_0\_10.xtc -o rmsf.xvg -oq rmsf.pdb -res -b 5000  
Then I typed ‘1 (Protein)’

The graph of ‘rmsf.xvg’ is as follows.

 ![스크린샷, 2021-07-13 22-43-31](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/31bd9d76da6926ba30b5b3d24de3f408246b56df.png)

My protein complex has 4 chains and it shows each chain starts from its 1st residue.  
But, I hope to get a continous graph.

[molecules]  
; Compound #mols  
Protein\_chain\_A 1  
Protein\_chain\_B 1  
Protein\_chain\_C 1  
Protein\_chain\_D 1  
SOL 12116  
NA 17

Is there any way to do that after MD, or should I renumber pdb file and do MD again?

Any advice would be greatly appreciated.  
Thanks in advance.

Regards,  
Suhyeok.

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<div class="post-metadata">

**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:** [July 13, 2021, 2:09pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-a-continous-rmsf-graph-for-mutiple-chains/2504/2 "2021-07-13T14:09:25Z")

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Analyze the chains separately using index groups.

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<div class="post-metadata">

**Author:** ![explodedpt](https://avatars.discourse-cdn.com/v4/letter/e/8baadc/32.png) [@explodedpt](https://gromacs.bioexcel.eu/u/explodedpt)\
**Post date:** [July 13, 2021, 11:30pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-a-continous-rmsf-graph-for-mutiple-chains/2504/3 "2021-07-13T23:30:14Z")

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Umm that’s a way!

It seems like that I should renumber to get continuous rmsf.

Anyway, thanks to the reply.