[gmx-developers] Always an error output and "usage" text even without error
delleske at avmatsim.de
Mon Apr 18 10:24:13 CEST 2016
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
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
-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
-[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 -
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