VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Mon Apr 23 2007 - 10:32:12 CDT

Hi Peter,

When I run the script with vmd -dispdev text -e script, it get killed after
the output "atomselect0", which should come from "set systm [atomselect top
all]". Then the program will stuck for a while and "get killed". When you
say "You can use a list or array to store the data and unpack it at the end
as desired." do you mean I can get all the lists for all the frames and all
the residues and then do the analysis? Because what I need to do is to
process all the lists per frame. And also I can release all the dcd
trajectory in memory with only lists remained, which should be more memory
efficient. Am I right?

Is there a simply command line to check whether two list have any element in
common and to combine two lists have elements in common to one "unique"
list? Thank you very much.

Jianhui

On 4/23/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Hi Jianhui,
> while we'd need a few more details (such as where it dies) to figure out
> exactly what is going on, I can recommend a couple of changes that
> should make this easier and more memory efficient:
>
> -Use lsort -unique instead of bothering to define a new procedure for
> removing duplicate elements from a list
>
> -Write your main analysis as nested loops instead of first creating all
> the selections you could possibly need and iterating over them, eg:
>
> for {set i 1} {$i <= 1536} {incr i} {
> set thiswatsel [atomselect top "water and within 5.5 of resid $i"]
>
> for {set j 0} {$j < $numfrm} {incr j} {
> $thiswatsel frame $j
> $thiswatsel update
> set closeresids [lsort -unique -integer [$thiswatsel get resid]]
> .....
>
> }
>
> $thiswatsel delete
> }
>
> You can use a list or array to store the data and unpack it at the end
> as desired.
>
> Peter
>
>
> Jianhui Tian wrote:
> > Hi all,
> >
> > I have a water box of 1536 molecules. Now what I want to do is to make
> > atomselect of each of the molecule and then get the residue list of
> > other molecules within some distance of each water molecule. The
> > problem is that the tcl code will get killed. I dont know the reason.
> > Is it due to the memory limitation. I only have 512 memory in my PC
> > now. How can I do what I want to do here? I also posted the code I
> > write about this part.
> >
> >
> > #########################################
> > #########################################
> > proc simplifylist {slist} {
> > set newlist { }
> > foreach elem $slist {
> > if {[lsearch $newlist $elem] == -1} {
> > lappend newlist $elem
> > }
> > }
> > set newlist [lsort $newlist]
> > return $newlist
> > }
> >
> > ########################################
> > # Load the trajectoty files.
> > mol new prmtop type parm7
> > mol addfile dcd type dcd waitfor all
> >
> > set numfrm [molinfo top get numframes]
> > set systm [atomselect top all]
> >
> > #######################################
> > #Get all the atomselect.
> > for {set i 1} {$i <= 1536} {incr i} {
> > set atom($i) [atomselect top "water within 5.5 of resid $i"]
> > }
> >
> > for {set i 0} {$i < $numfrm} {incr i} {
> >
> > ######### Get all the connected list for each of the water molecule.
> > for {set j 1} {$j <= 1536} {incr j} {
> > $atom($j) frame $i
> > $atom($j) update
> > set list($j) [$atom($j) get resid]
> > set list($j) [simplifylist $list($j)]
> > puts "frame $i residue $j: $list($j)\n"
> > }
> > }
> >
> > exit
> >
> >
>