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

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) keep the same. But I am pretty sure some of them are changing, as I look into the Timeline analysis for secondary structure.

So how to use VMD to see the secondary structures at different time frames? Is there an alternative software that can do this?


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