I am using VMD to visualise the secondary structure of protein here.

The trajectories are from my Gromacs simulation. Firstly I use File - New Molecule... to load the protein.gro file. Secondly I use File - Load Data into Molecule... to load my protein.xtc trajectories.

Then I use Cartoon to visulise the structure. As I drag the time frames, all the secondary structures (e.g. alpha-helix, beta-sheet) stay the same. But I am pretty sure some of them are changing, as I look into the Timeline analysis for secondary structure.


  1. how do I use VMD to see the secondary structures at different time frames?
  2. Is there an alternative software that can do this?
  • $\begingroup$ Try here: mattermodeling.stackexchange.com. There's way more VMD questions there. $\endgroup$ – user1271772 Dec 7 '20 at 2:55
  • $\begingroup$ Can I move my questions there? $\endgroup$ – lanselibai Dec 7 '20 at 15:35
  • $\begingroup$ copy and paste them. $\endgroup$ – user1271772 Dec 7 '20 at 16:00
  • $\begingroup$ I’m voting to close this question because it seems to be a better fit for another community. $\endgroup$ – gringer Jul 4 at 4:53