VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 03 2009 - 22:04:04 CDT

Hi,
  Have a look at the namdplot plugin source code attached to this email
and adapt it for your purpose.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 04, 2009 at 02:50:41AM +0000, Andres Morales N wrote:
>
>
>
>
> Dear VMD users:
>
>
> 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?
> Or anybody have some suggestion??
>
> Thanks a lot.
>
> Andres
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078