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
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?
Thanks a lot for @Stefan's help! It finally works! So follow Stefan's guide, and replace the
molid with the number under the
ID in the