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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 (X11/20090817)


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!


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