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

[Rudolf Weeber]

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