The simulation box is divided into five sections (from left to right): the inlet control volume, buffer region, membrane, buffer region, and outlet control volume. The system is periodic in the x and y directions, with walls at the ends of the z direction to prevent molecular exchange between control volumes without passing through the membrane. The control volumes are 5 nm thick in z direction, and the buffer region is approximately 4 nm thick. There is also a 1 nm thick gap between the control volume and the wall. As a result, the center of mass is only removed in the x and y directions. The membrane is fixed at the center of the box by imposing a position restraint on a single atom at the center of the polymer membrane. The membrane itself is flexible, modeled with harmonic bond, angle, and dihedral angle potentials. The approach described here is sufficient to maintain the integrity of the membrane. More details on how the membrane is modeled will be provided in the following section.