
From:  Vincent Ustach 
Subject:  Re: [ESPResSousers] DPD interaction 
Date:  Tue, 19 Nov 2013 13:07:29 0800 
Dear Vincent,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 lennardjones 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
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 twoparticle, respectively threeparticle collisions. Higher densities will also lead to higher particlecollision terms but not to such drastically diminished diffusion coefficients.
The application of the softconservative 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 CecamConference:
http://www.cecam.org/workshop0188.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/T101Hydrodynamics/talk2DPD.pdf
Hope this helps you!
Best,
Jens

================
Dr. Jens Smiatek
Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart
Germany
Office: 1.032
Phone: +49(0)711/685 63757
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