From: Wang Yi (
Date: Tue Jun 19 2012 - 15:13:48 CDT


This page ( contains everything you need: get two bond vectors, take the dot product, calculate the angle by arccos.

Yi (Yves) Wang
Duke University

On 2012-6-19, at 下午2:49, Prof. Eddie wrote:

> Hi all,
> I would like to see the distribution of a time-series of bond angles in vmd. I can make the label and use vmd's gui to plot the results of the bond angle as a function of frame. I've seen the distance script that also gives the distribution of the distances and I'd like to do the same for the bond angle. But I have no idea how to change the distance in the script (set simdata($i.r) [veclength [vecsub $com1 $com2]] )
> to the angle.
> Has anyone done this before or do you have some ideas?
> Thanks,
> Eddie