[gmx-users] Re:Shell scripts

[Mark Abraham]

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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>>
>>
>> -- 
>> 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
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
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