GROMACS version: 2021.5
GROMACS modification: No
I would like to calculate the tilt angle (I assume it is the angle the helix axis makes with the Z-axis) of a membrane-embedded helix over MD time. I tried helixorient, but am not quite sure how to interpret the output. I used an index file which contains the indices of the C-alpha atoms (30 residues) of the helix.
In the output tilt.xvg file, I got the first column in MD time, then 30 columns of numbers. I assume each column corresponds to one C-alpha of the helix. But why am I not getting just one tilt angle for the whole helix at each time point? Why do I get a number for each C-alpha? Please help - thanks.