From: Norman Geist (
Date: Mon Feb 02 2015 - 03:39:04 CST



you can use ssache from the VMD script library to 1st compute and visualize the secondary structure for all the frames. If you use linux you might be interested in the accelerated sscache_bunch version which is a lot faster in caching through.


Afterwards you’ll need a script that does the plotting using the stored SS data. Therefore you will have to know what your plot should look like, f.i. helix and sheet percentage or what exactly do you want?


Norman Geist.


From: [] On Behalf Of Vy Phan
Sent: Monday, February 02, 2015 8:21 AM
Subject: vmd-l: plot secondary structure of protein along trajectory.


Dear vmd user!

I want to get the plot of secondary structure of protein along trajectory.

How can I plot them? Could you please help ?

Thank a lot

Phan Vy