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

Justin Lemkul jalemkul at vt.edu
Mon Aug 14 17:12:08 CEST 2017

On 8/14/17 11:09 AM, ZHANG Cheng wrote:
> 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?
If you don't tell gmx rms to use the index (via -n), it won't.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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