VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 19 2010 - 21:40:52 CST

Hi,
  I'm guessing that you are running out of memory.
You probably didn't encounter it with the interactive run
simply because the trajectory hadn't finished loading yet.
You can verify that this is what is going on by telling VMD
to load all of the frames at once (check box in the GUI)
rather than loading them in the background. If your trajectory
is >= 4GB or close to it, you should be using the 64-bit VMD
(if linux) otherwise you'll need to skip some frames.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 19, 2010 at 07:33:33AM -0300, Alberto Sergio Garay wrote:
> Hi Axel
>
> Thank you very much for your time and help.
>
> >Hi all
> >
> >I'm running a tcl script to calculate a frequency of thymine piling up
> >during a MD simulation. When I load the trajectory in VMD (graphical mode)
> >and then run the script, everything is OK, but when I try to run vmd
> >without
> >open the graphical environment, the trajectory starts to be loaded, but
> >after some time, it gives me the message: killed.
>
> >>is it the exact same trajectory? <---
> yes, it's the same trajectory.
>
> As you recommend me, I run vmd in a debug mode. The debugger gave me
> some warning "No debugging symbol found", but it seemed to be working..
> After using "where", it only gave me the message:
> No stack
>
> Could you tell me what it does mean? Am I doing something wrong?
>
> Thank you in advance.
>
>
> --
> Dr. Sergio Garay
> Facultad de Bioquimica y Cs. Biológicas
> Universidad Nacional del Litoral
> Santa Fe - Argentina
> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> Argentina
> Ph. +54 (342) 4575-213
> Fax. +54 (342) 4575-221
>
>
> Mensaje escrito por: Axel Kohlmeyer <akohlmey_at_gmail.com>:
>
> >hi sergio,
> >
> >
> >On Thu, Nov 18, 2010 at 8:12 AM, Alberto Sergio Garay
> ><sgaray_at_fbcb.unl.edu.ar> wrote:
> >>Hi all
> >>
> >>I'm running a tcl script to calculate a frequency of thymine piling up
> >>during a MD simulation. When I load the trajectory in VMD (graphical mode)
> >>and then run the script, everything is OK, but when I try to run vmd
> >>without
> >>open the graphical environment, the trajectory starts to be loaded, but
> >>after some time, it gives me the message: killed.
> >
> >is it the exact same trajectory?
> >
> >this kind of message typically would appear if you are running out of
> >memory.
> >
> >in any case, the way how to debug this is the following:
> >start vmd in debug mode (vmd -debug)
> >and then launch vmd with: run -dispdev text -e myscript.tcl
> >
> >now you should be able to narrow down the location of the crash.
> >if it crashes and drops you back into the debugger. type: where
> >and then get back to us with the output of that command.
> >
> >cheers,
> > axel.
> >
> >>
> >>my script includes the directive waitfor all
> >>
> >>Could anyone give a clue about this problem? What am I doing wrong?
> >>Why the script works well under the graphical environment and not in
> >>command
> >>line?
> >>
> >>Below I paste the script
> >>
> >>mol new run_completo.gro
> >>mol addfile run_completo.xtc steps 1 waitfor all
> >>
> >>#Enter the name for the output file
> >>set filename1 "file_out.dat"
> >>
> >>#Distance cutoff between thymine rings
> >>set dist_cutoff 5.0
> >>
> >>set PI 3.14159265358979
> >>
> >>#Angle between normal vectors of close (within dist_cutoff distance)
> >>thymine
> >>rings
> >>set angle_cutoff 20.0
> >>
> >>#Extract frames from file
> >>set num_steps [expr [molinfo top get numframes] - 1]
> >>
> >>#Open files for writing
> >>set out [open $filename1 w]
> >>
> >>#Making an array of list of resids
> >>for {set j 1} {$j <= 16} {incr j} {
> >>       set r($j) {}
> >>       set Center($j) 0.0
> >>       #array over each atom selected
> >>       for {set k 1} {$k <=4} {incr k} {
> >>               set at($j,$k) {}
> >>       }
> >>}
> >>
> >>#Making an array of residues' piling ups
> >>for {set i 1} {$i <= 16} {incr i} {
> >>       for {set j 1} {$j <= 16} {incr j} {
> >>               set Pile($i,$j) 0
> >>       }
> >>}
> >>
> >>#Making selections
> >>set sel1 [atomselect top "resid 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30
> >>32
> >>and name CT2 NT1 NT2 CT5"]
> >>
> >>for {set frame 1} {$frame <= $num_steps} {incr frame} {
> >>$sel1 frame $frame
> >>$sel1 update
> >>
> >>puts "frame: $frame"
> >>
> >>#making a list of at. names and coordinates
> >>set at_names [$sel1 get name]
> >>set coords [$sel1 get {x y z}]
> >>
> >>       for {set i 1} {$i <= 16} {incr i} {
> >>               #Assign the first 4 elements of the list to a residue
> >>               set r($i) [lrange $coords 0 3]
> >>               #then delete the 4 first elements of the list
> >>               set coords [lreplace $coords 0 3]
> >>               #summing over resids
> >>               set Sum {0 0 0}
> >>               set at_idx 0
> >>               foreach b $r($i) {
> >>                       set at_idx [expr $at_idx + 1]
> >>                       set Sum [vecadd $Sum $b]
> >>                       set at($i,$at_idx) $b
> >>               }
> >>               set Center($i) [vecscale [expr 1.0 / 4] $Sum]
> >>               #puts "Center($i): $Center($i)"
> >>       }
> >>
> >>
> >>       for {set i 1} {$i <= 16} {incr i} {
> >>               for {set j 16} {$j > $i} {incr j -1} {
> >>                       set dist [veclength [vecsub $Center($i)
> >>$Center($j)]]
> >>                       if {$dist <= $dist_cutoff} {
> >>                               puts "dist: $dist"
> >>                               set v1 [vecnorm [vecsub $at($i,1)
> >>$at($i,2)]]
> >>
> >>                               set v2 [vecnorm [vecsub $at($i,3)
> >>$at($i,2)]]
> >>                               set N1 [veccross $v1 $v2]
> >>
> >>                               ####################################
> >>                               set v3 [vecnorm [vecsub $at($j,1)
> >>$at($j,2)]]
> >>                               set v4 [vecnorm [vecsub $at($j,3)
> >>$at($j,2)]]
> >>                               set N2 [veccross $v3 $v4]
> >>
> >>                               ######################################
> >>                               set angle [expr 180 - (acos([vecdot $N1
> >>$N2])
> >>* 180 / $PI)]
> >>                               puts "angle: $angle"
> >>                               if {$angle <= $angle_cutoff} {
> >>                                       set Pile($i,$j) [expr $Pile($i,$j)
> >>+
> >>1.0]
> >>                                       puts "Pile($i,$j): $Pile($i,$j)"
> >>                               }
> >>                               if {$angle >= [expr 180 -$angle_cutoff]} {
> >>                                       set Pile($i,$j) [expr $Pile($i,$j)
> >>+
> >>1.0]
> >>                                       puts "Pile($i,$j): $Pile($i,$j)"
> >>                               }
> >>                       }
> >>               }
> >>       }
> >>}
> >>#Normalizing by the number of frames
> >>#Making an array of residues' piling ups
> >>for {set i 1} {$i <= 16} {incr i} {
> >>       for {set j 1} {$j <= 16} {incr j} {
> >>               #puts "Pile($i,$j): $Pile($i,$j) --> num_steps: $num_steps"
> >>               set Pile($i,$j) [expr ($Pile($i,$j) * 1.0) / $num_steps]
> >>               puts "Pile($i,$j) after normalization: $Pile($i,$j)"
> >>       }
> >>}
> >>#writing the matrix of interations
> >>for {set j 1} {$j <= 16} {incr j} {
> >>puts $out "$Pile($j,1) $Pile($j,2) $Pile($j,3) $Pile($j,4) $Pile($j,5)
> >>$Pile($j,6) $Pile($j,7) $Pile($j,8) $Pile($j,9) $Pile($j,10) $Pile($j,11)
> >>$Pile($j,12) $Pile($j,13) $Pile($j,14) $Pile($j,15) $Pile($j,16)"
> >>}
> >>close $out
> >>quit
> >>
> >>Thank you in advance.
> >>
> >>Sergio
> >>
> >>--
> >>Dr. Sergio Garay
> >>Facultad de Bioquimica y Cs. Biológicas
> >>Universidad Nacional del Litoral
> >>Santa Fe - Argentina
> >>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> >>Argentina
> >>Ph. +54 (342) 4575-213
> >>Fax. +54 (342) 4575-221
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> >--
> >Dr. Axel Kohlmeyer
> >akohlmey_at_gmail.com  http://goo.gl/1wk0
> >
> >Institute for Computational Molecular Science
> >Temple University, Philadelphia PA, USA.
> >
> >
>
>
> 

-- 
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