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


From: Axel Arnold
Subject: Re: [ESPResSo-users] weird force between charged rods
Date: Thu, 20 Mar 2014 22:30:54 +0100
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.3.0

Oops, forgot to reply all... Here the answer:

the forces only give the forces from the ions, not the rod-rod force (or energy), since the constraints can't move. Therefore, you get attractive forces. You need to add the rod-rod force yourself (2 lbjerrum lz tau tau' / rho, where rho is the rod distance and tau the line charge densities).

Will add some comment to the UG.

Cheers,
Axel

On 20.03.14 19:22, Stefan Kesselheim wrote:
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, 
expected.
Cheers
Stefan

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


--
JP Dr. Axel Arnold
ICP, Universit├Ąt Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609




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