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Re: [ESPResSo-users] Weird results from P3M interaction?
From: |
Rudolf Weeber |
Subject: |
Re: [ESPResSo-users] Weird results from P3M interaction? |
Date: |
Wed, 31 May 2017 15:26:29 +0200 |
User-agent: |
Mutt/1.5.24 (2015-08-30) |
Hi Clemens,
On Wed, May 24, 2017 at 02:34:30PM +0200, Clemens Jochum wrote:
> > 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 is my impression that this is a rather non-standard interaction setup. My
suggestion would be to setup the system with interactions as described in my
previous mail, i.e., on a monomer-monomer basis rather than on an arm-arm
basis. Once that system behaves as expected, you can re-add more complexity. In
this way, it should become clear, where something goes wrong.
Regarding the correctness of the P3M method: Results for several electrostatics
methods agree (testsuite/python/coulomb_cloud_wall.py). There is of course, no
guarantee that this hold for all situations, but it would not be the first
place, I'd look.
Regards, Rudolf