VMD-L Mailing List

From: David Poger (d.poger_at_uq.edu.au)
Date: Tue Aug 05 2008 - 00:24:10 CDT

Thanks for the quick reply. Unfortunately, I still have a memory leak...
I added the commands "$jsel delete" and "unset jsel" after the "j" loop
and "$isel delete" and "unset isel" after the "i" loop though. Should I
delete the frames once the coordinates of each one has been read? If so,
how?

Thanks for any help

David

for {set i $Dom1_1 } { $i<=$Dom1_n } {incr i} {
    # Number of atoms in the residues of Dom1 which is selected
    set isel [atomselect top "resid $i"]

    for {set j $Dom2_1 } { $j<=$Dom2_n } {incr j} {
        set distm 1000

        foreach coordi [$isel get {x y z}] {
            # Number of atoms in the residues of Dom2 which is selected
            set jsel [atomselect top "resid $j"]

            foreach coordj [$jsel get {x y z}] {
                set dist [vecdist $coordi $coordj]
                if {$dist<$distm} {set distm $dist}
            }
        }
        # The array is in angstroem!!
        set sumdistij($i,$j) [expr $sumdistij($i,$j)+$distm]
        set sumdistij2($i,$j) [expr $sumdistij2($i,$j)+$distm*$distm]

       #Release memory!
        $jsel delete
        unset jsel
    }
    $isel delete
    unset isel
}

John Stone wrote:
> Hi,
> You must delete the atom selections that you're creating within
> the loops in your script. Specifically, you must add
> "$isel delete" and "$jsel delete" (for example) to your nested
> loops. This is the cause of your memory consumption problem.
> This is a frequently asked question, it comes up almost once every
> week or two.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 05, 2008 at 11:31:10AM +1000, David Poger wrote:
>
>> Hello
>>
>> I have written a Tcl script that basically reads a trajectory and for
>> each frame, finds the shortest distance between every single residue of
>> a first domain and every single residue of another domain in a protein.
>> The final matrix with all the minimal distances is written in an output
>> file. The script works fine... for 2 frames. In fact, after a few
>> minutes (~10-20 frames), I have to kill it as it fills up the memory of
>> the PC (32GB of RAM!!!). Is there any way to optimize this script
>> (release memory for example?). I know I have several nested loops but I
>> don't how to do differentlty and I have absolutely no knowledge in code
>> optimization!
>>
>>
>> Thanks a lot!
>> David
>>
>>
>> # In order to run it start vmd without graphical interface by typing
>> # $> vmd -dispdev text -e script.tcl
>>
>> #======================================================#
>> # TO BE EDITED #
>>
>> set grofile protein.gro
>> set trajfile traj.xtc
>> set outputfile traj_contact.dat
>>
>> # #
>> #======================================================#
>>
>>
>> set datafile [open $outputfile w]
>> puts $datafile [format "%1s%7s%8s%9s%9s" "#" "Res1" "Res2" "<d>" "rmsd"]
>>
>>
>> mol new $grofile
>>
>> # Residues in domains 1D and 2D
>> set Dom1_1 20
>> set Dom1_n 155
>> set Dom2_1 126
>> set Dom2_n 244
>>
>> for {set i $Dom1_1 } { $i<=$Dom1_n } {incr i} {
>> for {set j $Dom2_1 } { $j<=$Dom2_n } {incr j} {
>> set sumdistij($i,$j) 0
>> set sumdistij2($i,$j) 0
>> }
>> }
>>
>> #animate style once
>> mol addfile $trajfile waitfor all
>> set nframes [molinfo top get numframes]
>> puts "nframes=$nframes"
>>
>> # The 1st frame is the $grofile used for the topology so I don't use it
>> # That's why k starts from 1 and not 0
>> for {set k 1} {$k<$nframes} {incr k} {
>> animate goto $k
>> display update
>> puts "frame #$k"
>>
>> for {set i $Dom1_1 } { $i<=$Dom1_n } {incr i} {
>> # Number of atoms in the residues of Dom1 which is selected
>> set isel [atomselect top "resid $i"]
>>
>> for {set j $Dom2_1 } { $j<=$Dom2_n } {incr j} {
>> set distm 1000
>>
>> foreach coordi [$isel get {x y z}] {
>> # Number of atoms in the residues of Dom2 which is selected
>> set jsel [atomselect top "resid $j"]
>>
>> foreach coordj [$jsel get {x y z}] {
>> set dist [vecdist $coordi $coordj]
>> if {$dist<$distm} {set distm $dist}
>> }
>> }
>> # The array is in angstroem!!
>> set sumdistij($i,$j) [expr $sumdistij($i,$j)+$distm]
>> set sumdistij2($i,$j) [expr $sumdistij2($i,$j)+$distm*$distm]
>>
>> }
>> }
>>
>> }
>>
>>
>> for {set i $Dom1_1 } { $i<=$Dom1_n } {incr i} {
>> for {set j $Dom2_1 } { $j<=$Dom2_n } {incr j} {
>> set mean [expr $sumdistij($i,$j)/($nframes-1)]
>> set mean2 [expr $sumdistij2($i,$j)/($nframes-1)]
>> set msd [expr $mean2-$mean*$mean]
>> set rmsd [expr sqrt($msd)]
>>
>> puts $datafile [format "%8d%8d%9.3f%9.3f" $i $j [expr $mean/10]
>> [expr $rmsd/10]]
>> }
>> }
>>
>> close $datafile
>>
>> puts "Finished"
>>
>> exit
>>
>> --
>>
>> _________________________________________________
>> David POGER, Ph.D.
>> Postdoctoral Research Fellow
>> Molecular Dynamics Group
>> School of Molecular and Microbial Sciences (SMMS)
>> Chemistry Building (#68)
>> The University of Queensland
>> Brisbane, QLD 4067
>> Australia
>>
>> Email: d.poger_at_uq.edu.au
>> Tel: +61 7 3365 7562
>> Fax: +61 7 3365 3872
>>
>>
>> ** Notice: Unless stated otherwise, this e-mail represents only the views
>> of the Sender and not the views of The University of Queensland.
>>
>
> 

-- 
_________________________________________________
David POGER, Ph.D.
Postdoctoral Research Fellow
Molecular Dynamics Group
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
The University of Queensland
Brisbane, QLD 4067
Australia
Email: d.poger_at_uq.edu.au
Tel: +61 7 3365 7562
Fax: +61 7 3365 3872
** Notice: Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.