I have a chain of particles constrained in a spherical region. I want to add a tube to my sphere from which the chain can escape. To do that, I created a cylinder region and united it with my spherical region. Everything works great and my chain escapes if the cylinder’s top and bottom surfaces are closed. However, I need at least the bottom surface of my cylinder to be open so it can act as a tube and have the chain escape to the rest of the simulation space. When I use the “open” command on my cylindrical region, the particles I have inside my sphere act as if there is no cylinder at all. They just stay inside the sphere. How can I make the “open” keyword work with this?
Here are the lines I have for my regions:
region capsid sphere 0.0 0.0 0.0 8.2 side in units box
#region mycylinder y 0.0 0.0 1 -15 0 open 1 units box
region mycylinder cylinder y 0.0 0.0 1 -15 0 units box
region createhole union 2 capsid mycylinder side in
fix spherecylinder all wall/region createhole lj126 1 0.12 0.134695