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Re: [ESPResSo] Coarse Graining with a Gay Berne potential
From: |
Olaf Lenz |
Subject: |
Re: [ESPResSo] Coarse Graining with a Gay Berne potential |
Date: |
Mon, 12 Oct 2009 12:21:48 +0200 |
User-agent: |
Thunderbird 2.0.0.23 (X11/20090817) |
Hi!
Michael Winokur wrote:
I'm now at the point where I'm trying to use the GB potential for representing
a phenylene ring in a molecule. However I do not see how to implement a
dihedral interaction between biphenylene pairs. The simplest method I can
imagine is to specify a dipole direction for each GB unit and then use a
dipole-dipole interaction for the two particles which maps the more standard
dihedral interaction requiring four particle ids. I do not see anything in
the current Espresso interaction list that manages this (although it should
not be too difficult to add something like this to the code by someone that is
more familiar than I with the source code). Is there an existing method that
I ought use?
So far, there is no such interaction. To my knowledge, the GB potential
has not been used in any compounds with bindings, so far, but mostly for
liquid-crystal-like particles.
Using the dipole-dipole interaction is not advisable: it is a long-range
interaction, and therefore much slower than any short-range interaction,
and it is pretty bad in modeling bindings, would think.
I guess you will have to implement such a potential yourself. It is not
very complicated to create a new bond potential yourself. Have a look at
the implementation of FENE potential and the GB potential itself, and
you should be able to implement something that works.
The mathematics of that potential, however, might become tedious.
Good luck!
Olaf