Gmx rms will not write .dat file

User discussions
1

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:

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.

2

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.