VMD-L Mailing List
From: Meander Myself (ni1fios1_at_gmail.com)
Date: Thu Nov 20 2014 - 09:26:27 CST
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So, i'm using 'orient' to get the principal axis of inertia (long axis) for
an alpha-helix, using this script.....Well, its 2 short regions on the same
helix -HHHHHH--HHHHH 'proximal' and 'distal' respectively
cd ~/Desktop/Doctorate/A/A1/proximal
lappend auto_path ../../../../scripts/la1.0
lappend auto_path ../../../../scripts/orient
package require Orient
namespace import Orient::orient
set nf [molinfo top get numframes]
set outfile [open 0to2.dat w]
set del [atomselect top "index 37 to 59"]
for { set i 1 } { $i < $nf+1 } { incr i } {
$del frame $i
set J [draw principalaxes $del]
puts $outfile "[lindex $J 2]"
}
close $outfile
cd ../distal
set outfile [open 0to2.dat w]
set del [atomselect top "index 60 to 73"]
for { set i 1 } { $i < $nf+1 } { incr i } {
$del frame $i
set J [draw principalaxes $del]
puts $outfile "[lindex $J 2]"
}
close $outfile
The script outputs 2 vectors for evey timestep and i get the angle by
180-cos(a.b) in the usual way. These vectors correspond to the least
eigenvalue of the problem,
It's giving me some very dubious values - e.g. angles keep reversing say
60/120 degrees alternating within 1 timestep...
Does orient pick a direction vector ----> or <------ at random because my
selections are quite short?
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