VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 25 2006 - 22:55:10 CDT

Hannes,
  Can you send me a copy of the script that exhibits the problem
so I can have a look at it? I'm wasn't previously aware of any
memory leaks in VMD 1.8.5. In order to fix it I'll need to be
able to reproduce the problem locally, so having a copy of the
exact script you're using will be helpful. If there is a memory
leak, then it should turn up for me as well.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 25, 2006 at 11:10:48AM -0700, Johannes Mllegger wrote:
> John,
>
> this is a follow up to a thread posted Jan 05. I use VMD 1.8.5 on a
> Gentoo Linux system and I see the very same symptoms as Daniel has
> observed with the "sidechain" selection. My script calculates rmsd
> values per residue and when I use selections like "noh" "backbone"
> "not backbone" no problem. When I use the "sidechain" selection with
> the same script the %MEM use keeps increasing to >96 and the %CPU
> goes down to <5. Depending on the size of the system (number of
> frames, residues) VMD finally blows up and quits. I am getting around
> this by using the "not backbone" selection for now.
>
> -hannes-
>
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>
> Johannes Müllegger
> Enzyme Engineer
> Zymeworks Inc.
> 201 - 1401 West Broadway
> Vancouver, BC, Canada
> V6H 1H6
> Phone: 604 678 1388 -24
> Fax: 604 737 7077
> www.zymeworks.com
>
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>
>
>
> Daniel,
> Thanks for the note. I fixed a couple of memory leaks that used
> to exist in the old versions of VMD, can you try the same selection
> on one of the VMD 1.8.3 test builds and let me know if you experience
> the same problem still?:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jan 26, 2005 at 07:53:55PM -0500, Daniel Han wrote:
> >
> > Hello VMDers,
> > I am running a script that counts the number of contacts a residue
> has.
> > I wanted to limit the contacts, to only those that were near the
> > sidechain and not the backbone.
> >
> > While the two commands below, produce the same results:
> > set nearby [atomselect $mol "$seltext2 and within $dist of ((resid
> > $residue and not hydrogen) and (not backbone))" frame $i]
> > set nearby [atomselect $mol "$seltext2 and within $dist of ((resid
> > $residue and not hydrogen) and (sidechain))" frame $i]
> >
> > The second command uses up a large amount of memory, and the memory
> > usage will stay high even after the script is complete.
> > On the other hand, the first command uses a small to no amount of
> memory
> > at all, but takes much longer for the script to complete.
> >
> > I imagine it has to do something with short circuiting of
> commands ...
> > any ideas?
> >
> > Danny.
> >
> >
> 

-- 
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