Re: [ESPResSo-users] DPD interaction

[Dr. Jens Smiatek]

On 11/19/2013 08:02 PM, Vincent Ustach wrote:
> Hi everyone,
>
> I want to understand DPD in ESPResSo a little better. If I wanted to 
> obtain a diffusion coefficient for one colloid (say for a protein) in 
> a liquid on the order of 10^-7 what knobs would I turn? Is this 
> possible? Since DPD imposes friction on DIFFERENCES in velocities for 
> particles within the cut off radius, am I correct in thinking you need 
> a relatively crowded system to obtain that damping? For T = 1.0 and 
> volume fraction < 0.15 I am seeing diffusivity values higher than gas 
> particles.
>
> p.s. You may recall I am working with lattice Boltzmann to get 
> hydrodynamics. As such I am only looking for understanding.
>
>
>  inter 1 1 lennard-jones 1.0 0.30 0.33673 0.25 0
>  setmd time_step 0.001
>  setmd skin      0.4
>  thermostat dpd 1.0 1.0 0.16837
>
> etc...
>
>
> Best Regards,
>
> --Vincent Ustach

Dear Vincent,

whatever you do with DPD, it mostly behaves as a gas. This becomes 
specifically obvious by regarding the Schmidt number.
For such low volume fractions you described, the Boltzmann regime is 
present. For intermediate densities like rho = 3 to 10 sigma^{-3}, a 
mean field description is valid
which takes into account two-particle, respectively three-particle 
collisions. Higher densities will also lead to higher particle-collision 
terms but not to such drastically diminished diffusion coefficients.
The application of the soft-conservative DPD force is also not a good 
idea due to the fact that for higher particle densities crystallization 
effects would occur.
For all of these reasons, DPD would not be the method of choice for the 
considered system if you are really interested in correct diffusion 
constants.
The authors of a recent paper have suggested to use BD simulations for 
these kind of systems
http://www.pnas.org/content/107/43/18457.long
or Stokesian Dynamics
http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4817660

So therefore, you may have a look at these references.
Furthermore, if you are interested in DPD, you may also have a look at 
the talks of a Cecam-Conference:
http://www.cecam.org/workshop-0-188.html
Under "file" you' ll find a lot of elementary introductions.

There was also a talk at the Espresso summer school 2012:
http://espressomd.org/html/ess2012/Day4/T1-01-Hydrodynamics/talk2-DPD.pdf

Hope this helps you!

Best,
Jens

--
================
Dr. Jens Smiatek

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart
Germany

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