[gmx-users] How to use the index.ndx when running rms?

[ZHANG Cheng]

Dear Gromacs,
After running 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.


Then I run 
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in the same folder.


So how to use the index.ndx when running rms?


Thank you.


Yours sincerely
Cheng