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Re: [ESPResSo] Questions about Thermostat

From: Lorenzo Isella
Subject: Re: [ESPResSo] Questions about Thermostat
Date: Thu, 04 Sep 2008 22:48:18 +0200
User-agent: Mozilla-Thunderbird (X11/20080724)

Hello Torsten,
And thanks for your reply.

(2) In the simulations I ran, I start with a certain number of
monomers (i.e. the initial particles I place in the computational box)
which stick upon collisions thus giving rise to aggregates.
The diffusion coefficient of the resulting aggregate does not take
into account the fact that a monomer deep inside the aggregate is
"screened" by the surrounding monomers and hence feels a different
noise with respect to a "free" Brownian monomer.
I wonder whether the DPD thermostat in Espresso can somehow account
for that, but I am not sure it is a reasonable choice and would like
to know the opinion of someone on this list.

I'm not sure, if I understood your question correctly. Do you want to
apply different DPD prefactors (gamma and temperature) to particles
whether they are inside or outside of aggregates ?

Not exactly. Let us say that you have two aggregates each made up of 50 monomers (think of each aggregate as a structure consisting of 50 spherules). Aggregate A has a different shape than aggregate B (A almost looks like a sphere whereas B is elongated, chain-like). Physically, you would expect them to diffuse differently (in a quiescent fluid). The reason is that each monomer in aggregate A "feels" differently the fluid than in aggregate B. For instance, the inner monomers in aggregate B have a very small surface directly exposed to the fluid. But if I study their diffusion properties using Langevin thermostat (hence using Langevin equation), in the end I see no difference, the reason being that nothing in Langevin equation accounts for the screening of the inner monomers in an aggregate. Notice that I am not using the thermostat to model the coupling of the system with a thermal bath, but to investigate its coarse-grained dynamics (mesoscopic rather than microscopic description). Now, I wonder if the DPD thermostat can do what I need (which is not to model shear at this stage, but to make each monomer aware of the surrounding monomers within the aggregate, which should affect the aggregate diffusion properties).
Hope this clarifies what I am trying to do.


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