VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 30 2006 - 07:06:21 CDT

Hi Javier,
this is once again the dreaded atomselect memory leak... if you change
the inner loop to

{
    $Atom frame $FrameI
    puts $outfile [$Atom get {resname segname resid name index x y z}]
}

or

{
set Frame [atomselect top all frame $FrameI]

puts $outfile [$Frame get {resname segname resid name index x y z}]
$Frame delete
}

Things should work. The former is faster and should be preferred in this
case. The way you have it, though, you're spawning atomselect objects
that never get deleted, and likely running out of memory.
Peter

Lechuga, Javier wrote:
> Hello,
>
> Running the next script into VMD:
>
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> set Atom [atomselect top all]
> set FrameN [molinfo top get numframes]
> set outfile [open File.out w]
> puts $outfile "[$Atom num] $FrameN"
> for {set FrameI 0} {$FrameI<$FrameN} {incr FrameI 1} {
> set Frame [atomselect top all frame $FrameI]
> puts $outfile [$Frame get {resname segname resid name index x y z}]
> }
> close $outfile
>
>
> After 200 frames processed, I am getting the next error:
>
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> Runtime error!
>
> Program: C:\Program files\University of Illinois\VMD\vmd.exe
>
> This application has requested the Runtime to terminate in an unusual way,
> Please contact the application's support team for more information
>
>
> Any idea about what it could be or how can I solve this issue?
>
> Thank you
>