From: Daniel Möller (
Date: Mon Aug 27 2018 - 04:31:42 CDT



VMD normally just check the secondary structure once and will show this the whole frames. But there is scachebunch:

which is an improved version of sscache:


They’re going through your loaded trajectory and will save every secondary structure per frame (calculated with stride).


I don’t know if this are in the default installation, but you could load them from the links above. (stride should be default)





Daniel Möller



Von: <> Im Auftrag von Peter Mawanga
Gesendet: Montag, 27. August 2018 09:41
An: Vmd l <>
Betreff: vmd-l: Secondary structure representation stays static


Hello VMD users


I have a cluster of small peptides bound to a membrane surface and I would like to visualise the secondary structure changes in them over the simulation period.


I have run Timeline, and although I could see the secondary structure changes in the Timeline plot, but they are not reflected in the New Cartoon representation of the peptides over the simulation trajectory.


Could someone please suggest a way to overcome this issue? I am using VMD 1.9.3.