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Re: [ESPResSo-users] DPD interaction

From: Ulf Schiller
Subject: Re: [ESPResSo-users] DPD interaction
Date: Tue, 19 Nov 2013 22:10:32 +0100
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On 11/19/2013 09:20 PM, Dr. Jens Smiatek 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

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 all of these reasons, DPD would not be the method of choice for the
considered system if you are really interested in correct diffusion

Just a small addendum: There is a difference to be made between self-diffusion and diffusion of solute molecules. As long as one does not seek to reproduce a specific equation of state, a gas-like solvent is not in principle a problem. In fact, most mesoscopic methods (MPC, LB) have an ideal gas equation of state and can still produce correct diffusion coefficients. The challenge is more in modelling the colloid and its interactions with the solvent, and a simple point-like colloid is often not sufficient (for the reasons Jens explained). For DPD, the Schmidt number and transport coefficients have indeed a limited range, which does especially affect non-equilibrium properties of solute molecules, however, I'd expect the latter effect to be of less importance for colloids (w/o internal degrees of freedom) than for, e.g., polymers. In any case, Schmidt numbers up to 10^5 can easily be achieved using the Lowe-Anderson thermostat for DPD. Certainly, in a bulk system SD/BD would be more efficient, but isn't easily generalized to confined systems where HI become anisotropic. Of course, things are different in a melt/concentrated suspension when HI are screened and instead lubrication corrections may be needed. In my view, the Skolnick method does not address this situation satisfactorily, and I'd recommend checking results carefully against other methods, in case you are inclined to try.


Dr. Ulf D. Schiller                        Building 04.16, Room 3006
Institute of Complex Systems (ICS-2)       Phone:   +49 2461 61-6144
Forschungszentrum J├╝lich, Germany          Fax:     +49 2461 61-3180

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