VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Fri Nov 19 2010 - 04:33:33 CST

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.
>
>