<p dir="ltr">Hi,</p>
<p dir="ltr">There is also -nocopyright. See <a href="http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx.html">http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx.html</a></p>
<p dir="ltr">Mark</p>
<br><div class="gmail_quote"><div dir="ltr">On Mon, 18 Apr 2016 18:15 Justin Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
On 4/18/16 4:23 AM, Andreas Delleske wrote:<br>
> Dear Gromacs developers,<br>
><br>
> I am maintaining a test system that encloses test runs of GROMACS in our<br>
> environment - I hope it's not a FAQ.<br>
><br>
> I don't know anything about what exactly GROMACs does but what I see is:<br>
><br>
> When issueing these commands<br>
><br>
> grompp -f /some/folder/vacuum.mdp -c molecule_0.gro -p molecule_0.top &><br>
> out1.txt ; sync ; mdrun -s topol.tpr -rerun molecule_0.gro &> out2.txt<br>
> ; sync<br>
><br>
> although there is no error, my error file fills up with output like the<br>
> centered header and stuff like this (I cite only parts)<br>
><br>
><br>
> Option Filename Type Description<br>
> ------------------------------------------------------------<br>
> -f /some/folder/vacuum.mdp Input grompp input file with MD<br>
> parameters<br>
> -po mdout.mdp Output grompp input file with MD parameters<br>
> -c molecule_0.gro Input Structure file: gro g96 pdb tpr etc.<br>
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<br>
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.<br>
> -n index.ndx Input, Opt. Index file<br>
> -p molecule_0.top Input Topology file<br>
> -pp processed.top Output, Opt. Topology file<br>
> -o topol.tpr Output Run input file: tpr tpb tpa<br>
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
> -e ener.edr Input, Opt. Energy file<br>
> -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt<br>
><br>
><br>
> Why does this have to go in the error output? Can I turn it off?<br>
><br>
<br>
Users often find such logged information useful for verifying settings, as the<br>
defaults are displayed in the case of options that are not explicitly set. This<br>
can be meaningful when diagnosing issues.<br>
<br>
The output can be turned off (or at least, greatly reduced) by using the -quiet<br>
argument.<br>
<br>
> And then, an even bigger issue for me:<br>
><br>
> -maxwarn int 0 Number of allowed warnings during input<br>
> processing. Not for normal use and may generate<br>
> unstable systems<br>
> -[no]zero bool no Set parameters for bonded interactions without<br>
> defaults to zero instead of generating an error<br>
><br>
> .. and the I get two notes.<br>
><br>
> I understand that it is desired behaviour to print the notes into the<br>
> error output, my problem is that in the abovementioned text both words<br>
> "error" and "warning" occur - so when I grep the text for those<br>
> keywords, I get false positives.<br>
><br>
<br>
Meaningful errors and warnings are indicated by ERROR and WARNING, respectively,<br>
so grep for case-sensitive matches. For grompp, any number of errors or<br>
warnings will be fatal, so you can grep for "fatal" as well.<br>
<br>
-Justin<br>
<br>
> My question: Can this output be less verbose? Without the header? Can I<br>
> do something about it?<br>
><br>
> Many thanks -<br>
><br>
> Andreas<br>
><br>
><br>
><br>
><br>
><br>
<br>
--<br>
==================================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br>
<br>
Department of Pharmaceutical Sciences<br>
School of Pharmacy<br>
Health Sciences Facility II, Room 629<br>
University of Maryland, Baltimore<br>
20 Penn St.<br>
Baltimore, MD 21201<br>
<br>
<a href="mailto:jalemkul@outerbanks.umaryland.edu" target="_blank">jalemkul@outerbanks.umaryland.edu</a> | (410) 706-7441<br>
<a href="http://mackerell.umaryland.edu/~jalemkul" rel="noreferrer" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br>
<br>
==================================================<br>
--<br>
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</blockquote></div>