VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 26 2009 - 15:16:44 CST

Hi,
  It looks like you're failing to delete the atom selections
you're creating in your script. You need to have a
call to "$sel delete" inside that loop... That's probably
one of the reasons your memory use is not going down much.
Also, you should put the "frame0" selection and molecule
loading outside of the loop, otherwise you're killing your
machine...

Cheers,
  John

On Thu, Feb 26, 2009 at 04:00:53PM -0500, Fred (Rui FENG) wrote:
> Hi All,
>
> The manual says when tcl command "animate delete all" is executed, VMD
> will delete all the frames from the memory. But when I check the
> memory from the Windows Task Manager, the memory doesn't reduce much.
> Because I'm trying to read a 2.4 GB dcd file frame by frame to
> calculate RMSD, VMD will use up the memory. The Tcl code is below:
>
> # codes start
> set dcdfile C:/test.dcd
> set outfile [open rmsd.dat w]
>
> # rmsd calculation loop
> for { set i 100 } { $i <= 200 } { incr i } {
> animate delete all
> mol addfile $dcdfile type dcd first 0 last 0 step 1 filebonds off
> autobonds off waitfor all
> set frame0 [atomselect top "name N" frame 0]
>
> mol addfile $dcdfile type dcd first $i last $i step 1 filebonds off
> autobonds off waitfor all
> set sel [atomselect top "name N"]
> $sel frame $i
> $sel move [measure fit $sel $frame0]
> puts $outfile "$i [measure rmsd $sel $frame0]"
> puts $i
> }
> close $outfile
> animate delete all
> # codes end
>
> Do you know how to slove the out-of-memory problem? Thank you!
>
> Have a nice day!
>
> Fred 

-- 
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