VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 18 2010 - 08:28:41 CST

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.