Re: [ESPResSo-users] creating new shapes in ESPResSo

[Florian Weik]

Hi,

shapes in Espresso are additive, so you can not build up the desired shape from walls and cylinders. Also the cylinder shape is closed at the ends. But there exists a shape that is very close to what you want: The SimplePore shape consists of two walls with an cylindrical orifice between them. The only difference to what you are describing is that the openings are rounded. I think this will do for your purpose. The SimplePore is not yet in the main line of Espresso, but it is available from https://github.com/espressomd/espresso/pull/1295, and will be integrated soon; I'm working on that as we speak.

Hope that helps,

Florian

On Tue, Nov 14, 2017 at 8:44 PM Mohammadreza Niknam Hamidabad <address@hidden> wrote:

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
import 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.