[gmx-users] Re:Shell scripts

[lloyd riggs]

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...

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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