VMD-L Mailing List

From: Johannes Müllegger (hannes_at_zymeworks.com)
Date: Mon Sep 25 2006 - 13:10:48 CDT

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-

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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

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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.
>
>