VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 19 2010 - 06:27:46 CST

On Fri, Nov 19, 2010 at 5:33 AM, Alberto Sergio Garay
<sgaray_at_fbcb.unl.edu.ar> 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?

i don't know. is there a way you can make your files available for debugging?
this seems to be more complicated than it initially looked like.

axel.

>
> 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.
>>
>>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.