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[ESPResSo-users] creating new shapes in ESPResSo

From: Mohammadreza Niknam Hamidabad
Subject: [ESPResSo-users] creating new shapes in ESPResSo
Date: Tue, 14 Nov 2017 23:13:40 +0330

Dear all,

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
espressomd from espressomd.shapes import Cylinder
wall = Wall( dist= , normal=[ , , ] ) system.constraints.add(shape=wall, particle_type=0, penetrable=True)
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?

Best regards,
M. Reza Niknam H.

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