# Gmx rms will not write .dat file

**URL:** <https://gromacs.bioexcel.eu/t/gmx-rms-will-not-write-dat-file/11116>\
**Category:** User discussions\
**Created:** [January 22, 2025, 8:01pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-will-not-write-dat-file/11116 "2025-01-22T20:01:48Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dgoppenheimer](https://avatars.discourse-cdn.com/v4/letter/d/7ea924/32.png) [@dgoppenheimer](https://gromacs.bioexcel.eu/u/dgoppenheimer)\
**Post date:** [January 22, 2025, 8:01pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-will-not-write-dat-file/11116/1 "2025-01-22T20:01:48Z")

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GROMACS version: 2022.3  
GROMACS modification: Yes/No NO  
I am trying to generate a .dat file to use with t-SNE clustering and I have used the following command:

```auto
gmx rms -s protein.gro -f protein.xtc -o rmsd.xvg -bin rmsd.dat

```

I use 1 protein for least squares fit and 1 protein for rmsd calculation.  
The output files I get is only the rmsd.xvg file. The trajectory file and gro file have the water molecules removed and I have fit the trajectory to a reference structure, put it in a box, centered it. What do I need to do to get gmx rms to create the .dat file?  
Thank you!

UPDATE:

I believe I can convert the .xvg file to a .dat file by deleting all the header information. But gmx rms still does not write the .dat file.

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<div class="post-metadata">

**Author:** ![dgoppenheimer](https://avatars.discourse-cdn.com/v4/letter/d/7ea924/32.png) [@dgoppenheimer](https://gromacs.bioexcel.eu/u/dgoppenheimer)\
**Post date:** [January 28, 2025, 5:42pm UTC](https://gromacs.bioexcel.eu/t/gmx-rms-will-not-write-dat-file/11116/2 "2025-01-28T17:42:48Z")

</div>

Fixed it! I was using `gmx rms` incorrectly. As stated in the documentation, you use the `-m` flag to write the comparison matrix and then `-bin` will write the matrix to a `.dat` file.