thank you for the response. i tried to use dipole moment vector for the calculation
I used dipwatch gui to get dipole vector for the molecule from mol2 file
# frame dip_x dip_y dip_z |dip|
0 -0.05827735364437103 -1.521030306816101 -0.7441486716270447 1.6943100925406684
Then i used orient package to get (z) principle axis in vmd
set I [draw principalaxes $sel]
set A [orient $sel [lindex $I 2] {0 0 1}]
further, I can use dotproduct to get the angle between both vectors
proc angle { a b } {
set am [veclength $a]
set bm [veclength $b]
set dotprod [vecdot $a $b]
return [expr 57.2958 * acos($dotprod / ($am * $bm))]
}
Now I am confused about how to define the dipole vector and the vector corresponding to z only?
Can you help me with some short script or something?