First of all, I want to thank you guys for this awesome MD package. I've waited for a long time to work with python-based ESPResSo.
My question is:
I wanted to know how can I have a non-penetrable wall with a cylindrical membrane in the middle of it. I thought something like this will work:
A non-penetrable thick wall with a penetrable cylinder in the middle.
import espressomd from espressomd.shapes import Wall
import espressomd from espressomd.shapes import Cylinder
wall = Wall( dist= , normal=[ , , ] )
myShape = Cylinder(center=[, ,], axis = [, , ], direction = , radius= , length = )
myConstraint = system.constraints.add(shape = myShape, particle_type=p_type, penetrable=False)
But I think It's wrong. In this case we have two shapes that actually have overlaps.
In more general form I want to make more complicated membranes such as alpha-hemolysin. How can I do that?
And about the nonbonded interactions, how these shapes are simulated? Are they like a grid of particles?
M. Reza Niknam H.