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[ESPResSo] Re: analyze nbhood & Bond-angle Interactions

From: Lorenzo Isella
Subject: [ESPResSo] Re: analyze nbhood & Bond-angle Interactions
Date: Mon, 29 Oct 2007 18:40:53 +0100

Dear Peter,
I actually tried out your suggestion and I liked what I saw.
Before delving into the (controversial) choice of the expression of
the interaction potential for nanoparticles (most likely I will have
to use a tabulated potential; BTW: can it be capped?) there are
several other questions I need to address (of course I am asking them
to the whole Espresso list).
Some of them go beyond numerics and Espresso, but probably someone
knows the topical reference for that.
Let us say that I want to study the dynamics of N particles in the
Langevin thermostat, all of them interacting with a very deep
Lennard-Jones (LJ) potential.
1)At the beginning, I will have to cap the LJ potential after randomly
locating the particles.
Is there a recommendation for the choice of the cap value? Is it arbitrary?
2)In some of the tests I was running, VMD was showing the particles to
"stick" together and form a large aggregate. In some cases, the
aggregate would cross the box boundary (periodic boundary conditions
assumed) and part of it would re-enter the box somewhere else.
Is this a conceptual problem? I can easily cope with a single particle
exiting and being re-introduced, but I am not sure this is sound for a
large aggregate made up of tens of particles strongly bound (whose
structure is precisely what I want to study). In other words: what is
the recommendation for the box size? Is it simply fixed by the density
I want to reach?
3)How does one know that the solution has "converged"?
In other words: what are the indications that the time step, the box
size and the total time duration of the simulation have been properly
Is it perhaps the fact that some statistics of the results is
insensitive to e.g. halving the time step, doubling the box size while
keeping the density constant, and so on and so forth?
4)In the tutorial, I saw that Espresso actually creates a mesh. When
should one start being concerned with it? In case it matters, I
re-state my physical problem: diesel exhaust nanoparticles in hot air
are "kicked" randomly by air molecules and only once they get within a
certain distance (particle radius) from each other they "stick"
together (so far the easiest thing to do was to use a deep LJ

Many thanks


On 23/10/2007, Peter Kosovan <address@hidden> wrote:
> Dear Lorenzo
> In my opinion, using the bond-angle potential to represent non-spherical
> shape and angle-dependent interactions in the aggregation of colloidal
> particles is not the most natural choice. Moreover, using the FENE-type of
> bond for a colloidal system seems wierd to me as well. I would suggest a
> different workaround.
> First of all, I would suggest using lennard-jones type of a potential
> between the particles should suffice to stick them together rather than
> introducing a true bond between them. If you set epsilon_LJ>>kT, then once
> the particles find each other, they stick together. If you set epsilon_LJ
> comparable to kT, you also get a finite probability that a particle
> escapes from the cluster which seems to me a more physical picture of a
> colloidal system when compared to introducing non-breakable FENE bonds.
> The second suggestion is that you do not have to represent a single
> colloidal particle by a single particle in Espresso. In the simplest case,
> you can represent it by two espresso-particles forming a dumbbell (dimer),
> or you can build more complicated representations such as A-B-A trimer,
> with the A-B-A bond angle fixed. In this way, a colloidal
> particle of any shape can be represented and the individual
> espresso-particles play the role of interaction sites on the surface of
> the colloidal particle.
> With regards
> peter
> Peter Kosovan
> Department of Physical and Macromolecular Chemistry
> Faculty of Science
> Charles University in Prague
> Czech Republic
> address@hidden
> Tel. +420 221 951 290

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