I have performed MD simulation to a trans membrane protein using gromacs 2018. Can anyone provide me way to calculate the tilt angle of the protein relative to bilayer? Also how can I calculate the the rotation angle of the protein?
I have not been able to calculate with gromacs the angle of rotation of the transmembrane segments of a membrane protein, this is the order gmx helixorient, but I have not been able to obtain relevant information. I chose to use pymol to calculate the angle of rotation using a free script that you can find in the following link https://pymolwiki.org/index.php/RotationAxis I hope it is useful for you