Re: [ESPResSo-users] Weird results from P3M interaction?

[Rudolf Weeber]

Hi, 
On Tue, May 23, 2017 at 06:00:09PM +0200, Clemens Jochum wrote:
> I re-ran some simulations without Coulomb interaction and there the
> clustering does not occur, so it seems that the P3M method is indeed the
> cause. I will try to provide suitable mesh parameters to circumvent the
> tuning and see if that helps.
You can still use the tuning, but provide the mesh constant. 
> > The k-space part seems to be included, but looking at the code (e.g., in 
> > src/core/verlet.cpp:build_verlet_lsit()), my impression is that the 
> > short-range part (which is up to ~2.5 Bjerrum lengths in your system) is 
> > not.
> > Note that the short range part of p3m is implemented as a non-bonded 
> > interaction (sr/core/forces_inline.hpp:add_non_bonded_pair_force()).
> > What are the exclusions needed for? 
> I need the exclusions for the dendrimer: the LJ-interaction has an
> offset, that is a couple of times larger than the bond length. So I need
> to exclude the neighbouring particles from the LJ-interaction. I want
> them to keep interacting via Coulomb potential, though. Is there a way
> to do this?
I'm not sure I understnad your setup.
I suppose, you have two particle tyeps:
* particles making up the dendrimer (say type 0)
* salt ions (type 1)

Now, there would be the following lj interactions:
dendrimer-dendrimer (0,0): 
  either sigma=bond length, epsilon=few kT, cut_off=Something between 2^1/6 
bond length and more, depending on whether you want an attractive tail.
  or cutoff=bond_length sigma=cutoff /(2^(1/6)), in which case the bonds ould 
not be stretched by the lj potential
  


ion-ion (1,1): sigma=ion diameter, cutoff=2^(1/6) sigma, epsilon=few kT

dendrimer-ion (0,1): Also purely repulsive, with a sigma determined by a 
mixigngrule. Sigma could be larger than the dendrimer bond length

You can put charges on all particles as needed.

Is this actually your setup? It would not need exclusions, which is good, as 
they will probably remove the short range electrostatics for respective pairs 
of particles.

Regarding the clustering: have you checked your charges on the ions? With 
Lennard-Jones repulsion + strong electrostatic attraction, you might even get 
them to crystallize.
What do you get when comparing 
U =q1*q2/(sigma_ion/l_b)
to kT. Here, sigma_ion is the sigma from the ion-ion lj potential and l_b the 
Bjerrum length you chose (7, according to your p3m tuning output)

Regards, Rudolf