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