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Re: [ESPResSo-users] DPD interaction

From: Vincent Ustach
Subject: Re: [ESPResSo-users] DPD interaction
Date: Tue, 19 Nov 2013 13:07:29 -0800

Thank you Jens! I'll have a look at all of this.

--Vincent Ustach
  University of California, Davis

On Tue, Nov 19, 2013 at 12:20 PM, Dr. Jens Smiatek <address@hidden> wrote:
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


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
or Stokesian Dynamics

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:
Under "file" you' ll find a lot of elementary introductions.

There was also a talk at the Espresso summer school 2012:

Hope this helps you!


Dr. Jens Smiatek

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart

Office: 1.032
Phone: +49-(0)711/685 63757
E-Mail: address@hidden

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