GROMACS version: 2024.4
GROMACS modification: no
Hello !
I’m trying to run a simulation where the position of one atom is fixed while we pull away the other, and I want to pull it only in the Z axis. I’ve tried to use
pull-coord1-geometry = distance
pull-coord1-dim = N N Y
together, or
pull-coord1-geometry = direction
pull-coord1-vec = 0.0 0.0 1.0
together, and none of them worked. First, I’m not sure of the exact difference between these two groups of parameters. Second, although it only pulls the atom along the z axis, it stills allows it to move freely in the XY plane, and I only want it to move along the pull axis. In my understanding, this is what the vector parameter should do, but the atom still moves in all directions. I’m using pull-coord1-rate, so maybe that’s what slightly modifies how the vector parameter works.
Any help is greatly appreciated and I thank you for your time !