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

From: Mohammadreza Niknam Hamidabad
Subject: Re: [ESPResSo-users] creating new shapes in ESPResSo
Date: Wed, 15 Nov 2017 23:49:50 +0330

Dear Florian,
Thank you so much. Currently, the version of ESPResSo on GitHub doesn't have Pore shape, right?  When do you think the 3.3.2 version of ESPResSo and new shape module will be released? Is it before the Christmas?

Best regards,
M. Reza Niknam H.

On Wed, Nov 15, 2017 at 6:23 PM, Florian Weik <address@hidden> wrote:
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, and will be integrated soon; I'm working on that as we speak.

Hope that helps,

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
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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