VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 20 2016 - 02:37:41 CST

You produced a common memory leak with many atomselects which you never
clear.

After you no more need an atomselect object, you should call "delete" on it
to free memory.

 

Eg.:

 

set a [atomselect top all]

set list [$a get index]

$a delete; #<-------

 

So whats happening is that vmd gets killed for eating up all the memory.

 

Best of luck

 

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Amit Gupta
Gesendet: Dienstag, 20. Dezember 2016 07:31
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: Draw arrows in trajectory file

 

I want to draw come arrows in a lammps trajectory file, indicating movement
of certain vectors.

I have written script below, it works fine for single frame, but for more
than one frame, VMD crashes without any message (even in console). Can
anyone suggest a reason?

 

draw color yellow

##-----------Draw arrow subroutine from VMD website----------

 

proc vmd_draw_arrow {mol start end} {

    # an arrow is made of a cylinder and a cone

    set middle [vecadd $start [vecscale 0.75 [vecsub $end $start]]]

    graphics $mol cylinder $start $middle radius 0.1

    graphics $mol cone $middle $end radius 0.3

}

 

##--------------------------------------------------------------------------
------

 

set n [molinfo top get numframes]

set sel [atomselect top "all"]

set n_list [atomselect top "type 6"] #get indexes of all nitrogens in
molecules

set all_n_atoms [$n_list get index]

 

for {set i 0} {$i < $n} {incr i} {

     $sel frame $i

    foreach n_atom $all_n_atoms {

        set current_c_atom_index [expr $n_atom - 1] # get index of C
attached to N

        set end [lindex [[atomselect top "index $n_atom"] get {x y z}] 0]

        set start [lindex [[atomselect top "index $current_c_atom_index"]
get {x y z}] 0]

        draw arrow $start $end

    }

}

 

Sorry if certain logic seems slightly convoluted, still getting used to TCL!