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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.

So how do I use VMD to see the secondary structures at different time frames?

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Yes, It can. Just run this script in Extensions --> TK console of vmd before visualizing

proc structure_trace {name index op} {
      vmd_calculate_structure $index
}

trace variable vmd_frame w structure_trace
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