Problem with files being written and read by different versions of GROMACS

User discussions
1

GROMACS version: 2021.3
GROMACS modification: Yes/No

Hello all, GROMACS convert-tpr is currently giving me this error:

To clarify, I am running this through SBGrid where I have forced the setting of “2020.2_cu9.2.88” as my grimaces version using my SBGrid configuration file.

Has anyone seen anything similar before?

gmx convert-tpr, version 2021.3
Executable: /programs/x86_64-linux/gromacs/2021.3_cu10.2/bin/…/…/gromacs-2021.3-lzui/bin/gmx
Data prefix: /programs/x86_64-linux/gromacs/2021.3_cu10.2/bin/…/…/gromacs-2021.3-lzui
Working dir: /project2/arac/…
Command line:
gmx convert-tpr -s protein_md_1us.tpr -o protein_md_1us_ana.tpr

Reading file protein_md_1us.tpr, VERSION 2020.2 (single precision)
Note: file tpx version 119, software tpx version 122
/programs/share/capsules/lib/job.sh: line 120: 42440 Segmentation fault “SB_EXECFILE" "@”

2

Hi,
maybe this post helps

\Alessandra

3

There is a bug when calling convert-tpr with only -s and -o (possibly since 2021.3).

Depending on which function of convert-tpr you want to use, there may be some workarounds:

  • If you want to extend the runtime, use option -until, -extend, -nsteps (see help: -h for details on what they do).
  • If you want to extract a subset, or, if you want to update the tpr version but do nothing otherwise (that is, exactly what you seem to be doing with that command line), you have to specify an index file also. You can select group 0 to output the whole system. For use in script, you can use something like echo 0 | gmx convert-tpr -s in.tpr -o out.tpr -n index.ndx