VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jun 03 2009 - 22:29:45 CDT

On Thu, 2009-06-04 at 02:50 +0000, Andres Morales N wrote:
>
>
> Dear VMD users:

dear andres,
 
> I minimize 100 structures gotten from molecluar dynamics (I used NAMD
> for that). One of the outfiles of each one is a .log file, which
> contains information about energy minimization, like that:
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP TOTAL2
> TOTAL3 TEMPAVG
> ENERGY: 0 1337.4596 713.5074 247.3819
> 7.8238 -11987.9289 5524.7427 689.0913
> 0.0000 0.0000 -3467.9223 0.0000
> -3467.9223 -3467.9223 0.0000
> INITIAL STEP: 1e-006
> GRADIENT TOLERANCE: 48654.6
> PRESSURE: 1 0 0 0 0 0 0 0 0 0
> GPRESSURE: 1 0 0 0 0 0 0 0 0 0
> ENERGY: 1 1333.9980 713.0198 247.3724
> 7.8159 -11988.7232 5070.9980 689.0540
> 0.0000 0.0000 -3926.4651 0.0000
> -3926.4651 -3926.4651 0.0000....
>
>
> I need to extract the initial and final total energy from each
> strcuture (from each .log file).
> Are there any script to do that?

some simple "unix-plumbing" does the trick already, e.g.:

( grep '^ENERGY:' xxxx.log | head -1 ; grep '^ENERGY: xxxx.log \
 | tail -1 ) | awk '{ print $12 }'

> Or anybody have some suggestion??

you can check out the NAMD plot plugin
and try to see, if you can rip some pieces
of tcl script out of it that does the same
as above.

cheers,
   axel.

>
> Thanks a lot.
>
> Andres
>
>
> ______________________________________________________________________
> Invite your mail contacts to join your friends list with Windows Live
> Spaces. It's easy! Try it! 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.