[gmx-users] analysing helix dynamics

[jayant james]

Hi all,
During MD simulations of a protein,I find that there are two helices
switch periodically from being parallel and perpendicular to each
other.  I'd like to plot out the orientation of these two helices with
respect to each other, is there a command to extract this information?

JJ

http://www.chick.com/reading/tracts/1071/1071_01.asp