VMD-L Mailing List

From: Adelene Sim (adelene_at_stanford.edu)
Date: Sat Nov 11 2006 - 18:11:22 CST

Hi, I'll like to know if it is possible to plot a graph for the number of
hydrogen bonds versus time in a system where a protein is being stretched
(e.g. like the stretching Deca-alanine tutorial). Also, is there a way to
measure the percentage helicity (and also plot a graph) with time?

 

I've been told that these can be done in the Extension menu of VMD, but I
can't seem to find any way to do that, except perhaps plot bond energies,
which isn't really what I want.

 

Thanks in advance!

 

Adelene