VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 20 2007 - 16:41:17 CDT

Hi,
  Are you being careful to delete selections within your loops?
Unsetting variables is insufficient to prevent memory use from increasing,
you must actually call '$sel delete' for each and every selection you created
if you're creating them within loops. I'm be willing to review your
plugin code if you send it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 21, 2007 at 12:25:33AM +0300, Θωμας Ευαγγελιδης wrote:
>
>
> Hi,
> I have written a plugin for VMD (~320 lines of code) which creates smaller dcd
> and psf files from bigger ones by taking into account only the atoms that are
> within $cutoff distance from the macromolecule. The program works fine with a
> small number of frames, but when this number exceeds 10 it crashes. At first I
> thought that there was a memory leak so I filled up the program with unset
> commands, but the problem still remained. After that I split it in 2 parts. The
> first produces the "truncated frames" in pdb format, and the second finds which
> atoms must be included in each one in order the final frame-pdbs to contain the
> same intact residues and the same atoms. The program works by creating,
> concatenating and deleting many pdbfiles. I tried to run the first part, close
> the VMD, restart it and run the second, but the program always crushed at the
> same point of the second part. In example when I used 11 frames it crashed at
> frame 10, and when I
> used 15 frames from the same initial dcd it crashed at frame 8.
> Does anyone has any idea about what is going wrong? I could send the code if
> that would help.
>
> Thomas 

-- 
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