GROMACS version: 2020.2
GROMACS modification: No
In visualizing all of my simulations thus far with both PyMOL and VMD, I have noticed an odd behaviour of lysine amino hydrogens, where they appear to completely close and then open up almost like a flower.
I have extracted frames where the hydrogens appear to be closed together using ‘gmx trjconv’, and when I analyze these frames, the hydrogens are always open as they should be in a tetrahedral geometry. This leads me to believe that the odd behaviour is just an artifact of the visualization method.
I was wondering, has anyone else noticed this during the visualization of trajectories? Does anyone know what might be the cause of this?