VMD-L Mailing List

From: Manali Mehendale (manali_at_adrik.bchs.uh.edu)
Date: Sat Dec 08 2007 - 15:09:47 CST

Hi,

I tried changing my script in the following way, but it still doesnt get
past ~800 molecules. Can you please let me know specifically where the
problem is and how i can change it ?
Thanks in advance.
Manali

set outfile1 [open length1.dat w];
foreach filename [lsort -dictionary [glob *.mol2 ]] {
mol load mol2 $filename
set distAB 0
set sel [atomselect top all]
set s [$sel get index]
set length [llength $s]

for {set i 0 } {$i < $length } { incr i} {
for { set j 0 } { $j < $length} {incr j} {

set sel1 [atomselect top "index $i"]
set sel2 [atomselect top "index $j"]
set A [lindex [$sel1 get { x y z}] 0]
set B [lindex [$sel2 get { x y z}] 0]

lappend distAB [vecdist $A $B]
}
}
set result [lindex [lsort -decreasing $distAB] 0]
puts $outfile1 $result
$sel delete
$sel1 delete
$sel2 delete
mol delete all
}
close $outfile1

On Fri, 7 Dec 2007, Axel Kohlmeyer wrote:

> On Dec 7, 2007 2:15 PM, Manali Mehendale <manali_at_adrik.bchs.uh.edu> wrote:
> > Hi,
> >
> > I am trying to calculate the length of multiple (thousands) small
> > molecules (upto 100 atom length).
> > My script works perfect for few molecules but when i try to process
> > thousands it takes up too much memory and freezes up the system.
> > Any help will be greatly appreciated.
>
> manali,
>
> please check out the tips and hints at:
> http://biocore.ks.uiuc.edu/biocore/biofs/VMD%20(Public)/tips/tclscripts.html
>
> your script is creating many atom selections and not deleting them
> => memory leak
> => freeze due to excessive swapping
>
> axel.
>
> >
> > Thanks,
> > Manali
> >
> >
> > The script is as follows:
> >
> > set outfile1 [open length.dat w];
> > set m 0
> > foreach filename [lsort -dictionary [glob *.mol2]] {
> > puts $filename
> > mol new $filename type mol2 waitfor all
> > molinfo top set drawn 0
> > incr m 1
> > }
> >
> > for {set k 0 } {$k < 4000 } { incr k} {
> >
> > set distAB 0
> > set sel [atomselect $k all]
> > set s [$sel get index]
> > set length [llength $s]
> >
> > for {set i 0 } {$i < $length } { incr i} {
> > for { set j 0 } { $j < $length} {incr j} {
> >
> > set sel1 [atomselect $k "index $i"]
> > set sel2 [atomselect $k "index $j"]
> > set A [lindex [$sel1 get { x y z}] 0]
> > set B [lindex [$sel2 get { x y z}] 0]
> >
> > lappend distAB [vecdist $A $B]
> > }
> > }
> > set result [lindex [lsort -decreasing $distAB] 0]
> > puts $outfile1 $result
> > }
> > close $outfile1
> >
> >
>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>