VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 13 2006 - 10:24:21 CST

Hi,
  You should be calling $sel delete inside the innermost loop, in the same
scope where you're creating the selection! The memory hogging is almost
certainly a result of delaying that $sel delete until all of
the loops are overwith, which causes all those selections (except the
last one) to be "leaked"..

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 13, 2006 at 02:10:16PM +0000, Leandro Martínez wrote:
> Dear VMD users,
> I need to visualize the the kinetic energy in each time-step of my
> simulation.
> I have written the velocity file for each step with NAMD and converted it
> to pdb file. Then I made a simple script that reads this velocity file,
> computes
> the kinetic energy per atom and puts it in the "user field" of each atom, in
> each frame of the trajectory (dcd) file. Everything seems to be working
> fine,
> unless for the fact that I can't load all data because it seems that using
> the "user field" is very memory demanding. In principle what I am loading is
> only a single real number for each atom, for each frame, and, therefore, it
> should not require much more memory than the trajectory itself, which I
> can load very quicky (the system has only 5000 atoms). However,
> my computer gets very slow and I cannot pass from frames 30 or 31 while
> filling the "user field". Bellow I attach the script I'm using for doing
> this, it
> is based on a script written by John Stone I got from this mail list. The
> reading
> of the velocity file is very fast, but the script gets extremely slow in the
> next
> loop and I cannot finish my analysis. Any help on this subject is
> appreciated.
> Thank you very much,
> Leandro.
>
> -----------The script: ------------------------------------
> set numframes [molinfo top get numframes]
> set numatoms [molinfo top get numatoms]
> puts "Opening velocity file..."
> set file [ open ./velocities2.pdb r ]
> set file [ read $file ]
> set file [ split $file "\n" ]
> set i 0
> puts "Reading velocity file... "
> foreach line $file {
> if { [ string range $line 0 3 ] == "ATOM" } {
> incr i
> set vx [ string range $line 30 37 ]
> set vy [ string range $line 38 46 ]
> set vz [ string range $line 47 54 ]
> set v2 [ expr $vx*$vx + $vy*$vy + $vz*$vz ]
> set kinetic [ expr $v2 / 2. ]
> set ek($i) $kinetic
> }
> }
> #The next step is slow:
> puts "Setting up atom colors..."
> set k 0
> for {set i 0} {$i<$numframes} {incr i} {
> puts "Setting User data for frame $i ..."
> for {set j 0} {$j<$numatoms} { incr j } {
> incr k
> set sel [atomselect top "index $j"]
> set mass [$sel get mass]
> animate goto $i
> $sel frame $i
> $sel set user [ expr $mass * $ek($k) ]
> }
> }
> $sel delete
> ---------------------------------------------------------------------
>
>
> ---------------------------------------------
> Leandro Martinez
> Institute of Chemistry
> State University of Campinas, Brazil
> http://www.ime.unicamp.br/~martinez/packmol
> -------------------------------------------- 

-- 
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