Thanks! I also came to that realization. Your point really sums up well

every point is both above and below both edges

This is what I was trying to say in my first post. Well really thank you, I will give this a shot.

That seems to be what I need to be able to prevent water from entering the membrane region.

I can define the boundaries of the membrane region and then I just want to reflect all waters. But doesn't the customExternalForce use periodic coordinates? So, the direct implementation would not be correct.

Sure, here is the expression of the flat-bottom potential
The z-upper and z-lower bounds will be defined by the head groups of the lipids.

**Edit: Fixed typo in energy equation

I am seeking to implement a CustomExternalForce applied to water particles to prevent them from penetrating the membrane in the early stage of the simulation. This is simple with a flat-bottom harmonic potential, however the issue that I find is with PBC. This excerpt from the CustomExternalForce do...