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
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Tanya Johannsen
> Sent: Friday, July 07, 2006 09:56
> To: amber.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
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 09 2006 - 06:07:26 PDT
