VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 04 2008 - 21:44:48 CDT

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. 

-- 
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