VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 21 2011 - 09:48:08 CST

Hi,
  Your script is not deleting the atom selections it is creating
after it finishes using them. You should be calling "$s delete"
after you're done using them. If you type the command "atomselect list"
you will see that your script is not cleaning up all of the selections it
creates.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 21, 2011 at 04:13:18PM +0100, Tim Meyer wrote:
> dear all,
> in a former thread a memory leak was reported (and reported fixed)
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16658.html
>
> running a small skript analyzing waters in a trajectory where i loop for
> each frame through all ~1000 water molecules (see below) does however
> accumulate memory (version 1.8.7 and 1.9b1) and leads to a crash after ~20
> frames (1.5GB of RAM)
> i tried to free memory using "unset s" didn't seem to work.
> any suggestions on how to free memory within the loop?
>
> thanks in advance
>
> tim
>
>
>
> mol addfile TRAJ/1cqy.1.netcdf type netcdf first 0 last 999 step 1 waitfor
> -1
> set wat [atomselect top "water and oxygen"]
> mol representation vdw
> mol addrep top
> set num_frame [molinfo top get numframes]
> puts "have $num_frame frames"
> for { set frame 0 } { $frame < $num_frame } {incr frame} {
> animate goto $frame
> puts $frame
> foreach inx [$wat list] {
> set s [atomselect top "noh and within 3.5 of index $inx"]
> }
> } 

-- 
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