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

From: Limbach, Hans Joerg, LAUSANNE, NRC-FS
Subject: RE: [ESPResSo] Re: analyze nbhood & Bond-angle Interactions
Date: Wed, 31 Oct 2007 08:34:42 +0100


Nothing. The periodic boundary condition (PBC) (and with that the
reentering) is just one way to treat the boundary problem. If you want
to simulate a system at a finite density you have to fix a volume and in
some way specify the boundary of this volume. You can either do this by
placing some kind of wall at the boundary or use PBC. 
As Burkhard stated already, this reentering does not change your
aggregate. The radius of gyration (Rg) will be the same as before.
Actually Espresso keeps track of all events when particles cross the box
boundary. For analysis like Rg Espresso uses the real coordinate of the
particles, which can be outsite of the primary simulation box. When you
visualize your system with VMD you can choose wether you would like to
have the particles folded into the primary simulation box or not (see
options for write_pdb).
If this still sounds kind of magic to you I suggest to read some basic
textbook on MD simulations, e.g. Frenkel/Smith or Allen/Tildesley.


> -----Original Message-----
> From: address@hidden 
> [mailto:address@hidden On Behalf Of 
> Lorenzo Isella
> Sent: mardi, 30. octobre 2007 18:59
> To: address@hidden
> Cc: address@hidden
> Subject: Re: [ESPResSo] Re: analyze nbhood & Bond-angle Interactions
> Hello,
> And many thanks for your reply.
> I got hold of the paper, but I am slightly concerned about 
> the point quoted below:
> > Sounds all reasonable to me. I don't see a fundamental difference 
> > between a re-enetering particle and a re-entering cluster.
> You see, one of the things I am interested in is to study how 
> the radius of gyration of an aggregate scales with the number 
> of particles.
> Ideall, starting with N particles I will end up with a single cluster.
> Now, what happens when I evaluate the radius of gyration of a 
> cluster which is being re-entered in the box? I refer to the 
> situation in which I have only a single large cluster I want 
> to study in detail.
> This is what is making me worried and I will try to study it 
> directly soon.
> Kind Regards
> Lorenzo
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