align atoms along axis

Installing the scripts

To use the principal axis scripts, you will need to follow these steps:

1. Download orient.tar.gzand la101psx.tar.gz. The latter is a linear algebra package by Hume Integration Software; you can look at the La homepage for more information.
2. Unpack the scripts

     gunzip orient.tar.gz  tar xf orient.tar  gunzip la101psx.tar.gz  tar xf la101psx.tar

3. Add the following lines to your .vmdrc to make it easy to load the packages; replace "/home/paul/scripts/" with the directory in which you unpacked the packages:

     lappend auto_path /home/paul/scripts/la1.0  lappend auto_path /home/paul/scripts/orient

Aligning a molecule to its principal axes

Load the molecule into vmd, and run the following commands to align the first, second, and third principal axes to the x, y, and zaxes.

  package require Orient  namespace import Orient::orient  set sel [atomselect top "all"]  set I [draw principalaxes $sel]  set A [orient $sel [lindex $I 2] {0 0 1}]  $sel move $A  set I [draw principalaxes $sel]  set A [orient $sel [lindex $I 1] {0 1 0}]  $sel move $A  set I [draw principalaxes $sel]

You may want to use the principal axes (stored in I) for other purposes than alignment, or modify the script to get information about the moments of inertia.

Author

Paul Grayson [e-mail]