How to implement trjcat?

[sperezconesa]

Hello,

Suppose I want to feed to files to trjcat. I tried this but didn't work:

import gmxapi as gmx

a = gmx.commandline_operation(
    "gmx",
    arguments=["trjcat", "-nooverwrite"],
    input_files={"-f": ["s0/traj_comp.xtc", "s1/traj_comp.xtc"]},
    output_files={"-o": "cat.xtc"},
)
a.run()
print(a.output.erroroutput.result())

Is there a good solution?
Thank you very much!
Best,
Sergio

[sperezconesa]

Nevermind, this works the problem was -nooverwrite should be -cat. My input files have the same time stamps and that's why it looked as if only one file was processed!

[sperezconesa]

In any case, the possibility of giving lists should be documented, which maybe it is. Just leaving this here as a reminder.

[eirrgang]

Yes. Very good point.

Related issues include

• https://gitlab.com/gromacs/gromacs/-/issues/3136
• https://gitlab.com/gromacs/gromacs/-/issues/3141
• https://gitlab.com/gromacs/gromacs/-/issues/3693

There were some proposed documentation updates that don't seem to have ever been merged or ported to the new issue tracking system, and I should revisit that. (issue 3136 dates from before the migration from Gerrit and Redmine to GitLab).

Of course, you are welcome to submit a merge request through https://gitlab.com/gromacs/gromacs/-/merge_requests with any notes that you have already identified as useful.

I will close this issue when I have re-posted the previously proposed documentation revision. If I can request your review of the proposed change, please let me know your GitLab ID and/or subscribe to https://gitlab.com/gromacs/gromacs/-/issues/3136