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

[Peter Košovan]

Hi Clemens,

comparing your Mayavi and VMD visualizations, I anticipate that each atom in your vmd box is visualized once. But some of them remain inside the original box and others are in some of the periodic copies.

In the writevcf function of the TCL interface there was a switch -folded which would result in what you observed in Mayavi. Your vmd visualization uses the unfolded coordinates.

Greetings,

peter

On Wed, Jun 28, 2017 at 11:26 AM, Clemens Jochum <address@hidden> wrote:

Dear all,

I figured out what the problem was or rather that there was no problem at all.

I decided to use a different tool for visualization and noticed that VMD not only shows the original simulation box but also the adjacent PBC boxes. For some reason only a part of the atoms is visualized in these additional boxes. And strangely the dendrimer is only shown in the original simulation box. So the clustered counter-ions around the dendrimer from the original box seemed to form clusters on their own in the additional PBC boxes. I attached some screenshots.

Thanks for your all your help and advice!

Best,
Clemens

On 01.06.2017 15:10, Florian Weik wrote:

Hello Clemens,

1) The error in P3M is not translation invariant (only on average), so in principle it can cause such effects. If you want to find out you can move the particle relative to the mesh an see if anything changes. I would recommend you to use a slightly larger mesh (maybe 32), and see if the effect goes away. The tuning result looks odd to me, this could be a bug in the tuning.go

As Rudolf was pointing out, you can fix the mesh and still tune the other parameters, simply by providing a mesh (p3m tune mesh 32 32 32 accuracy ...).

2) During the tuning process, the runtime of the force calculation is measured. The warning means that the variance of the samples was untypically big, this usually means that there

that something else on the machine is interfering with your espresso process. This can lead to a non-optimal tuning results but has no influence otherwise. This is an effect of the environment and not of the P3M parameters.

Otherwise, what Rudolf is saying.

Cheers,

Florian

On Wed, May 31, 2017 at 3:27 PM Rudolf Weeber <address@hidden> wrote:

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

--

Dr. Peter Košovan

2nd bMIS Workshop, May 14-19 2017 www.bmis.cz

Department of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
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