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 <[email protected]>
An: Discussion list for GROMACS users <[email protected]>
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 <[email protected]>
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 <[email protected]>
An: Discussion list for GROMACS users <[email protected]>
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs <[email protected]>
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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--
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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