make_ndx unexpectedly missing velocities
Summary
In gmx 2023.1 make_ndx does not work with tpr files for energy minimization, but used to do that in 2021.5 (maybe also later). Here is what happens:
BMC-7YTVT946V:dAT$ gmx make_ndx -f em/em.tpr -o tst
:-) GROMACS - gmx make_ndx, 2023.1 (-:
Executable: /Users/ermar499/bin/gmx/2023.1/bin/gmx
Data prefix: /Users/ermar499/bin/gmx/2023.1
Working dir: /Users/ermar499/Projects/RNA/maketst/dAT
Command line:
gmx make_ndx -f em/em.tpr -o tst
Reading structure file
Reading file em/em.tpr, VERSION 2023.1 (single precision)
Reading file em/em.tpr, VERSION 2023.1 (single precision)
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Program: gmx make_ndx, version 2023.1
Source file: src/gromacs/fileio/tpxio.cpp (line 3028)
Fatal error:
No v in input file
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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make_ndx should not need velocities and this seems like an unnecessary change of behaviour, so I would call it a minor bug.
I tested doing the same with a tpr file generated with gmx 2021.5 from the same input, and then make_ndx worked as expected. This suggests that grompp has changed in what it puts in the tpr files, but make_ndx has not been updated to fully deal with that.
Exact steps to reproduce
To reproduce:
gmx make_ndx -f em.tpr -o xna.ndx <<EOF
q
EOF
To make the tpr-file (attached, along with the files needed to generate it):
gmx grompp -f em.mdp -o em.tpr -c salty.pdb -p salty.top
For developers: Why is this important?
If this is a bug, (1) what happens, and (2) what did you expect to happen?
make_ndx ends with an error. I expected make_ndx to not need velocities.
Relevant input files, logs and/or screenshots
em.tpr salty.pdb salty.top em.mdp
Also see output in the summary above.