[gmx-users] Re:Shell scripts

[Tsjerk Wassenaar]

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
>>> --
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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