[gmx-users] Re:Shell scripts

[lloyd riggs]

Thanks,

and thanks to Tsjerk.

Stephan

-------- Original-Nachricht --------
> Datum: Fri, 06 Jul 2012 20:04:48 +1000
> Von: Mark Abraham <Mark.Abraham at anu.edu.au>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Re:Shell scripts

> On 6/07/2012 6:27 PM, lloyd riggs wrote:
> > Yes,
> >
> > I was just going over them individually, then cat into a single spread
> sheet, which I can use awk to do combos, $1+$2+$16+$233...etc...
> 
> With Tsjerk's suggestion, and g_energy -xvg none, you can have such a 
> "spread sheet" from one .edr file written in one go.
> 
> Mark
> 
> >
> > Its still alot of files but easier to manipulate with complex .ndx files
> than just using g_energy every time...mostly time saving when you exceed
> 10 simulation or more.  Still, having to re-learn some basic awk, gawk, cat
> and piping skills from 12 years ago is a pain, but the simple things are
> invaluable with gromacs I would say.  Without them you would become so bogged
> one might hit insanity levels...
> >
> >
> > Thanks
> >
> > Stephan Watkins
> > University of Bern-Inselspital
> >
> >
> > -------- Original-Nachricht --------
> >> Datum: Fri, 6 Jul 2012 07:09:16 +0200
> >> Von: Tsjerk Wassenaar <tsjerkw at gmail.com>
> >> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Betreff: Re: [gmx-users] Re:Shell scripts
> >> Hey,
> >>
> >> I'd probably go for something like:
> >>
> >> for ((i=1; i<...; i++)); do echo $i 0 | g_energy ...; done
> >>
> >> Note the additional 0 to make g_energy exit. The (( )) has been in
> >> bash for ages, so that shouldn't be a problem.
> >>
> >> I notice that in the working construct you used 'traj_x.edr', while in
> >> the earlier ones, you used 'traj_${i}.edr'. If you try to extract all
> >> energy terms from a single .edr file, you can also use
> >>
> >> echo $(seq 1321) 0 | g_energy -f traj_x.edr -o stuff.xvg
> >>
> >> and then parse the columns out of the .xvg file.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >> On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
> >> wrote:
> >>> On 6/07/2012 7:25 AM, lloyd riggs wrote:
> >>>> Dear All,
> >>>>
> >>>> Thank you,
> >>>>
> >>>> I finally got this to work on the other PC after four hours...
> >>>>
> >>>> i=1
> >>>> while [ $i -le 1322 ]
> >>>> do
> >>>> g_energy -f traj_x.edr -o ${i}.xvg << EOF
> >>>> ${i}
> >>>>
> >>>> EOF
> >>>> i=$(($i+1))
> >>>> done
> >>>>
> >>>> Still can not figure out the difference, or why one works on one PC
> and
> >>>> not the other?
> >>>
> >>> Probably different bash versions, as your Ubuntu could well be more
> >> recent
> >>> than some version on a server at work. Try bash --version. If so, poke
> >> your
> >>> system admins to make an up-to-date bash available for you, even if
> not
> >> as
> >>> the system default.
> >>>
> >>> Mark
> >>>
> >>>
> >>>> Stephan (in Rainy Switzerland)
> >>>>
> >>>> -------- Original-Nachricht --------
> >>>>> Datum: Thu, 5 Jul 2012 22:25:06 +0200
> >>>>> Von: Elton Carvalho <eltonfc at if.usp.br>
> >>>>> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>>>> Betreff: Re: [gmx-users] Re:Shell scripts
> >>>>> On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs <lloyd.riggs at gmx.ch>
> >> wrote:
> >>>>>> Does any one know why, or have some other scripts...
> >>>>>>
> >>>>> My suggestion would be something in the lines of
> >>>>>
> >>>>> #!/bin/bash
> >>>>>
> >>>>> for i in $(seq 2121) ; do
> >>>>> g_energy -f traj_${i}.edr -o ${i}.xvg <<< "${i} 0"
> >>>>> done
> >>>>>
> >>>>> ===
> >>>>>
> >>>>> Notice the "in" keyword right after 'i'.
> >>>>>
> >>>>> I used a subshell to invoke the program 'seq', which generates a
> >>>>> sequence from 1 to the given argument, so we don't depent om how
> these
> >>>>> other constructs with ((; ; )) work among different versions of
> bash.
> >>>>>
> >>>>> I also suggest replacing the here-document by a here-string, but
> >>>>> that's personal taste. You may or may not have problems with older
> >>>>> versions of bash
> >>>>>
> >>>>> Greetings from a foggy Groningen,
> >>>>> --
> >>>>> Elton Carvalho
> >>>>> Tel.: +55 11 3091-6985/6922
> >>>>> Dept Física dos Materiais e Mecânica
> >>>>> Instituto de Física
> >>>>> Universidade de São Paulo
> >>>>> P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
> >>>>> --
> >>>>> gmx-users mailing list    gmx-users at gromacs.org
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> >>>
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> >>
> >>
> >> -- 
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> -- 
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> 
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