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Re: [ESPResSo-users] weird force between charged rods

From: Stefan Kesselheim
Subject: Re: [ESPResSo-users] weird force between charged rods
Date: Thu, 20 Mar 2014 19:22:47 +0100

Dear Fabien,
I'm not sure if force the rod constraint was checked recently. It might well be 
possible that it is counted, for example, with the wrong sign. I believe I 
wrote the constraint force stuff for repulsive surfaces, but I'm not very sure 
about the forces of the rod constraint. Instead of the rod constraint I have 
always been using a line of particles. This could be an easy check. 
On the other hand: What are your system parameters? If you have DNA and 
trivalent ions at room temperature, like-charged attraction is, for example, 

On Mar 20, 2014, at 5:56 PM, Fabien Paillusson <address@hidden> wrote:

> Hi,
> I am simulating an apparently simple system with two infinite charged and 
> similar  rods (as constraints) embedded in two cylinders (as constraints) 
> neutralized by counterions in a 3d periodic box.
> When I run this system with P3M and look at density maps for instance, they 
> look totally fine and fit with my intuition of the physics going on in there. 
> However, when I try to compute the force on the rods (with the force 
> constraint command), I always get an attractive result while it should be 
> repulsive!
> I have tried to change many things including accuracy of the P3M method, size 
> of the box to prevent periodic images to interact with one another or rod 
> charge density so that I get below the Manning condensation threshold and 
> then I have naked charged rods interacting within a uniform background of 
> opposite charges and I always get the same attractive force whatever I do.
> Any idea on what could be going on?
> Thank you very much for any kind of help you could provide.
> Best,
> Fabien Paillusson
> Departament de fisica fonamental
> Universitat de Barcelona
> Marti i Franques, planta 3 i 4,
> ES-08028, Barcelona
> Personal webpage

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