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
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