AMBER Archive (2006)

Subject: RE: AMBER: script to extract data from minimization .out file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jul 08 2006 - 10:47:17 CDT

Hi Tanya,

You should try to learn scripting using grep and awk. These two commands in
combination are exceptionally powerful and will allow you to extract just
about any data you would want. E.g. the following will give you a file with
two columns where the first column is the step and the second column the
energy.

grep -A1 " ENERGY " minimization.out | grep -v " ENERGY " | grep " "
| awk '{print$1,$2}' > energy.dat

xmgrace energy.dat

It is quite easy to vary this to obtain other data as well. E.g. if you
wanted the RMS force instead of the energy you just change the $1,$2 to
$1,$3.

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Tanya Johannsen
> Sent: Friday, July 07, 2006 09:56
> To: amber_at_scripps.edu
> Subject: AMBER: script to extract data from minimization .out file
>
> Dear AMBER community:
>
> Does anyone have a script that can extract information
> (such as ENERGY) from a minimization .out file and put
> it in a data file that can be easily plotted? If
> anyone has such a script, I would be very grateful if
> I could borrow it. I looked at the listserv archive
> and tried the "plotamber" program that was suggested,
> but it doesn't seem to work on AMBER 8.
>
> Thank you very much in advance for any suggestions.
>
> Tanya
>
>
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