Re: [ESPResSo] Questions about Thermostat

[Lorenzo Isella]

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.
Cheers

Lorenzo