GROMACS version: 2023
GROMACS modification: No
I am trying to pull a carbon nanotube across a bilayer and want to align it along the z-axis. Using [ angle_restraints_z ] directive is probably the best way to do this. For this, an atom pair needs to be defined under [ angle_restraints_z ] directive. The nanotube edge towards membrane has, let’s say, 10 atoms. I can define diagonally opposite atoms as atom pairs 1 and 6, 2 and 7, and so on. I was wondering if adding a single atom pair will be sufficient or should I add multiple atom pairs for better alignment?
Thanks,
Raman