Thanks for the reply,
My main problem a syntax error as all of em are similar, but I get the
languages confussed sometimes. This worked;
#!/bin/bash
i=1
for ((i=1;x<=1322;i+=1)); do
g_energy -f energy.edr -o ${i}.xvg << EOF
${i}
EOF
done
for everything in the energy file based on indexed components.
I had finally written b efore giving up
#!/bin/bash
i=1
for (i=1;x<=1322;i+=1); do
g_energy -f traj_5.edr -o $i.xvg << EOF
${i}
EOF
done
Which is just a python script.
Thanky again
Stephan Lloyd Watkins
-------- Original-Nachricht --------
> Datum: Fri, 9 Mar 2012 11:47:09 -0700
> Von: Oliver Stueker <ostue...@gmail.com>
> An: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Betreff: Re: [gmx-users] Re:g_energy
> Hi Stephan,
>
> Have a look at:
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> something like this should work:
> ----------8><----------schnipp----------><8----------
> #!/bin/bash
> for i in Temperature Pressure ; do
> g_energy -f ener.edr -o ${i}.xvg << EOF
> ${i}
>
> EOF
> done
> ----------8><----------schnapp----------><8----------
>
> creating Temperature.xvg and Pressure.xvg assuming there are terms
> named like this in your ener.edr file.
> The braces around the i might not be necessary in this case, but don't
> hurt either.
>
> Best,
> Oliver
>
> On Fri, Mar 9, 2012 at 08:00, lloyd riggs <lloyd.ri...@gmx.ch> wrote:
> >
> > Dear All,
> >
> > Is there a way to either supress the interactive portion of g_energy and
> print out everything listed, or pass it to something more automated? MY
> problem, I spent an hour or three trying to just write an automated four
> line shell or python script to extract all the terms listed based on index
> files.
> >
> > The error comes as I can not pass a variable i once the interactive
> portion of the g_energy is invoked (I get error $i, i '$i', "$i", etc.. does
> not match a pattern or whatever as an error each time). Basically try
> getting a few dozen terms from an energy file, times 20 to 100 necessary
> runs...
> >
> > Sincerely,
> >
> > Stephan Lloyd Watkins
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