VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2008 - 14:45:49 CDT

Hi,
  You didn't attach your script, but from the description you've given,
it sounds to me like your script looping over frames, likely creating
atom selections but not deleting them after each loop iteration.
Make sure that you call "$sel delete" for each atom selection you
create within a loop iteration. If you search the mailing list archive
you will see that this topic comes up quite frequently.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 16, 2008 at 04:34:40PM -0300, Alberto Sergio Garay wrote:
> Hi
>
> I am using VMD to calculate a cylindrical density around a particular
> molecule in a lipid bilayer model. I have 10 ns gromacs trajectory
> (20.000 frames) to study. My script is not so complicated to take so
> long time to finish its task. Is it OK that the hard disk increases
> its work as the number of frames increases?. Sometimes the PC hang up.
> I am working in a Intel core2duo PC, with 2 Gb of RAM memory under
> Fedora core 6 linux OS.
> Is there any web site where I can take some pieces of advice to
> improve my tcl/tk scripting?
>
> Thank you in advance
> --
> Dr. Sergio Garay
> Facultad de Bioquimica y Cs. Biológicas
> Universidad Nacional del Litoral
> Santa Fe - Argentina
> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> Argentina
> Ph. +54 (342) 4575-213
> Fax. +54 (342) 4575-221
>
>
>
>
> 

-- 
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