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

[Clemens Jochum]

Dear Rudolf,

thanks again for your reply.

> 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.

In my system there are monovalent ions at room temperature. I don't
think that they should form crystals. I also observe this phenomenon for
a saltless system, which only contains the negatively charged dendrimer
and positive counter-ions. So the free ions actually only repel each other.

> 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)

U = 1 * 1 / ( 4 / 7 ) = 7 / 4 = 1.75 kJ/mol
kT = 2.478 kJ/mol
So the thermal energy is larger by a factor of approx. 1.5.

> 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

To clarify:

The units in the dendrimer are polymer-like chains of several monomers
(see attached snapshot). The monomers in these chains are bound by a
harmonic bond with l_b = 3.4. I also have a harmonic angle bond, which
accounts for the stiffness of the chains. The LJ-interaction is not
needed for the interaction of neighbouring monomers, but for the
interaction between the chain-like arms of the dendrimer.

The parameters of the LJ interaction are:

sigma = 4
r_off = r_mon + r_mon - sigma = 14
r_cut = 2^1/6 * sigma

So it is a shifted WCA-potential that looks like:

4 * epsilon * (sigma / (r - r_off))^12 - (sigma / (r - r_off))^6 if
r_off < r < r_off + r_cut

and it is 0 otherwise.

Because the harmonic bond forces neighbouring monomers to be around the
point of divergence (r = r_off = 14 = 4.12 * l_b) of the LJ-potential I
encountered some problems. This is why I want to exclude the 4 nearest
neighbours from the LJ-interaction.

It's kind of an intricate model, I hope I could make it comprehensible.

Best Regards,

Clemens

On 23.05.2017 18:27, Rudolf Weeber wrote:
> 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
>
>
>
>
>

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