Re: [ESPResSo-users] DPD

[Stefan Kesselheim]

Dear Dusan,

On Sep 11, 2014, at 4:07 PM, Dudo <address@hidden> wrote:

> Dear Jens,
> 
> thank you very much for the lead.
> 
> Well, so I've compiled in a feature for "TUNABLE_SLIP"
> and I have set up interactions: inter $cid $idpolym tunable_slip $temperature 
> $gamma_L $r_cut_L $timestep .....
> I have turned the flag to 2: constraint cylinder center $cx $cy $cz axis $cnx 
> $cny $cnz radius $crad length $clength direction $cdirection type $cid 
> reflecting 2 .....
> as Stefan suggested, and I'm trying with the parameters from your paper on 
> polyelectrolytes J. Phys Chem B 2010..
> Now I see you have used explicit solvent with density 3.75, while modelling a 
> chain of 20 beads.
> In my case this would mean zillions of solvent particles..
> Well at the begining Chris asked me, why would I do add explicit particles - 
> so.. is there a way around?

The particle numbers that you will need are necessary are considerable but OK. 
For a chain of 20 beads, the radius of gyration is probably around 5, and thus 
you need a box size of 10, and 20 is still doable. With a density of 1, you'll 
have 1k to 8k particles. That should be enough to perform the measurements, 
especially as you probably don't need too many steps to get a meaningful 
mobility. 

In principle you can use even lower densities, but at some point the mean free 
path of the particles becomes comparable to the box size, and then you are in a 
region where you should be sure what you are doing.

The strength of the hydrodynamic interaction, anyways, depends in the 
"hydrodynamic radius" of the particles. This is the size of a sphere with the 
same diffusion coefficient as an isolated particle with the same viscosity. If 
this quantity is too small (~1/(6 pi visc D), then hydrodynamics will be weak.

Cheers and good luck
Stefan