GROMACS version: 2024.1-dev
GROMACS modification: No
I am pulling two proteins from each other using their CoM vector aligned to the z-axis. I have removed the [fz] positional restraints in the mobile group, since I will be pulling in the z direction. I have kept the [fx fy] restraints, since I don’t want any secondary structure disruption during pulling. Furthermore, the direction of the pulling stays constant, as in the protein doesn’t drift in the x or y directions and the secondary structure doesn’t break. I still think that removing the [fz] positional restraints is adding a bias. Should I continue my sMD simulations like this or is it completely wrong?
Thanks in advance.