# Why is the order of amino acids in the output diagram of "gmx mdmat" messed up?

**URL:** <https://gromacs.bioexcel.eu/t/why-is-the-order-of-amino-acids-in-the-output-diagram-of-gmx-mdmat-messed-up/808>\
**Category:** User discussions\
**Created:** [September 13, 2020, 6:39am UTC](https://gromacs.bioexcel.eu/t/why-is-the-order-of-amino-acids-in-the-output-diagram-of-gmx-mdmat-messed-up/808 "2020-09-13T06:39:12Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![M.Yaghoubzad](https://avatars.discourse-cdn.com/v4/letter/m/96bed5/32.png) [@M.Yaghoubzad](https://gromacs.bioexcel.eu/u/M.Yaghoubzad)\
**Post date:** [September 13, 2020, 6:39am UTC](https://gromacs.bioexcel.eu/t/why-is-the-order-of-amino-acids-in-the-output-diagram-of-gmx-mdmat-messed-up/808/1 "2020-09-13T06:39:12Z")

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GROMACS version: 2020.3  
GROMACS modification: No

Hello

I did the “gmx mdmat” command as follows:

gmx mdmat -f md\_0\_1.xtc -s md\_0\_1.tpr- meaning mdmat.xpm -frames mdmat2.xpm -no mdmat.xvg

But in the output diagram, which I attached, the order of the amino acids on the x and y axes is disturbed. What is the problem? And how can I fix the error?!

 ![mdmat](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/58198a5f9cae8c52e838d86f9933362ef662d0e0.png)

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [September 15, 2020, 3:56pm UTC](https://gromacs.bioexcel.eu/t/why-is-the-order-of-amino-acids-in-the-output-diagram-of-gmx-mdmat-messed-up/808/2 "2020-09-15T15:56:17Z")

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Hi,  
maybe [gmx xpm2ps](http://manual.gromacs.org/documentation/current/onlinehelp/gmx-xpm2ps.html) can help you to visualize better your matrix.  
Alessandra