VMD-L Mailing List

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Mon Jan 08 2007 - 10:22:25 CST

Thanks Marcos,

As you said, adding the following lines to the code

$sim1 delete
$sim2 delete
$all delete

solved the problem.

Saludos,
Leonardo

On 1/8/07, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu> wrote:
>
>
>
> Hi Leonardo,
>
> you must use "$sel delete" in order to free the memory used by the
> atomselect command. Have a look at the box "Atom selections inside loops"
> in the last part of the VMD tutorial
> (
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html#SECTION00045000000000000000
> )
>
> Saludos,
> Marcos
>
> On Mon, 8 Jan 2007, Leonardo Sepulveda Durán wrote:
>
> > Hello. I have 3 systems simutated at different temperatures. For each
> > System-Temperature pair I have 20 simulations started from different
> random
> > seeds. I would like to calculate, for each 20-simulation group, the
> rmsds
> > between all trajectory pairs. I wrote a script to do this:
> >
> > # cycle ovel all simulation temperatures
> > foreach temp { 300 400 450 500} {
> >
> > # Cycle over all systems
> > foreach name { paa pac pan} {
> >
> > # load the 20 trajectories for each temperature and type of system
> > for {set i 1} {$i <= 20} {incr i} {
> > mol load psf ./$temp/din-$temp-$name-$i.psf dcd
> > ./$temp/din-$temp-$name-$i.dcd
> > }
> >
> > # Obtain the index of the top molecule (the last loaded)
> > set molnum [molinfo top]
> >
> > # define a counter for the traj-traj comparisons
> > set counter 0
> >
> > # Main calculation cycle. For each temperature and system, this
> code
> > calcule all the trajectory-
> > # trajectory rmsds, and then print the information to independent
> > files. The "for" loops decrease their
> > # indexes as the provided trajectory number is the last one
> > for {set i $molnum} {$i >= [ expr $molnum - 20 + 1 ] } {incr i -1} {
> > for {set j [ expr $i - 1] } {$j >= [ expr $molnum - 20 + 1 ] }
> > {incr j -1} {
> >
> > incr counter
> >
> > set num_frames [molinfo top get numframes]
> >
> > # make selection with all the atoms
> > set all [atomselect $i all]
> >
> > # Calculate the rmsd between frames k of 2 trajectories
> > for {set k 0 } {$k < $num_frames} {incr k } {
> >
> > # select the structures to be compared
> > set sim1 [atomselect $i "protein" frame $k]
> > set sim2 [atomselect $j "protein" frame $k]
> >
> > # do the alignment
> > set trans_mat [measure fit $sim1 $sim2]
> > $all move $trans_mat
> >
> > # measure RMSD between frames
> > set rms [measure rmsd $sim1 $sim2]
> >
> > # define rmsd array numbering
> > set h [expr $k + 1]
> >
> > set rmsd($h) $rms
> > }
> >
> > puts "\t$counter $i $j"
> >
> > # open output file
> > set outfile [open ./rmsd/$name-$temp-$counter.dat w]
> > for {set m 1} {$m <= $num_frames} {incr m} {
> > puts $outfile [format "%5d%7.3f" $m $rmsd($m)]
> > }
> > close $outfile
> > }
> > }
> >
> > unset sim1
> > unset sim2
> > unset all
> > unset rmsd
> > unset rms
> > unset h
> >
> > # delete all the loaded trajectories
> > mol delete all
> >
> > }
> > }
> >
> > I put the script above in a file called rmsdv1.0.tcl, and ran the script
> > with the command "vmd -dispdev text -e rmsdv1.0.tcl".
> >
> > It works without any trouble when I use 5 simulations instead of 20. In
> the
> > later case, the calculation dies out without any explanation besides
> writing
> > "killed" in the console. During the calculation, each iteration becomes
> > slower, so I think that the problem is asociated to memory usage. I dont
> > know how the memory is used during the computation, but is reasonable
> that
> > all the iterations where calculated at the same rate. It seems that
> after a
> > pairwise comparison the compared simulations remain in memory, I tried
> to
> > solve the problem using the "unset" statements at the end of the script,
> but
> > it seems to have no effect at all. Maybe the problem is another, any
> help
> > from a tcl programmer could help me.
> >
> > Thanks in advance.
> >
> > Leonardo Sepulveda
> > Universidad de Chile
> >
>