[gmx-developers] Always an error output and "usage" text even without error

[Andreas Delleske]

Dear Gromacs developers,

I am maintaining a test system that encloses test runs of GROMACS in our
environment - I hope it's not a FAQ.

I don't know anything about what exactly GROMACs does but what I see is:

When issueing these commands

grompp -f /some/folder/vacuum.mdp -c molecule_0.gro -p molecule_0.top &>
out1.txt ; sync ; mdrun -s  topol.tpr -rerun molecule_0.gro &> out2.txt
; sync

although there is no error, my error file fills up with output like the
centered header and stuff like this (I cite only parts)


Option     Filename  Type         Description
------------------------------------------------------------
  -f /some/folder/vacuum.mdp  Input        grompp input file with MD
parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c molecule_0.gro  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt.  Index file
  -p molecule_0.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o      topol.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file
-ref     rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt


Why does this have to go in the error output? Can I turn it off?

And then, an even bigger issue for me:

-maxwarn     int    0       Number of allowed warnings during input
                            processing. Not for normal use and may generate
                            unstable systems
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error

.. and the I get two notes.

I understand that it is desired behaviour to print the notes into the
error output, my problem is that in the abovementioned text both words
"error" and "warning" occur - so when I grep the text for those
keywords, I get false positives.

My question: Can this output be less verbose? Without the header? Can I
do something about it?

Many thanks -

Andreas