VMD-L Mailing List

From: Amit Gupta (amit__at_outlook.in)
Date: Tue Dec 20 2016 - 00:31:18 CST

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!