Odd Behaviour of Lysine Amino Hydrogens in Trajectory Visualization

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?

Best regards,
Josh Hayden

I have never seen this. Are you applying any sort of smoothing to the trajectory? If so, you’re only seeing interpolated positions, and since the H atoms will rotate around quite a bit even when the heavy atoms are relatively slow-moving, they will appear to behave bizarrely.

I have been applying smoothing to all of my trajectories, so that must be it.

Thank you!