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
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.
- how do I use
VMDto see the secondary structures at different time frames?
- Is there an alternative software that can do this?