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Re: [ESPResSo] ESPResSo Digest, Vol 29, Issue 8

From: Michael Winokur
Subject: Re: [ESPResSo] ESPResSo Digest, Vol 29, Issue 8
Date: Tue, 13 Oct 2009 10:51:39 -0500
User-agent: KMail/1.12.1 (Linux/2.6.30-1-486; KDE/4.3.1; i686; ; )

Hello Olaf and all,

I'm sorry but my description wasn't quite clear.  The "dipole" function serves 
only to give a preferred orientation to pairs of bonded oblate particles.  
This orientation would then be used to calculate the canonical dihedral 
interaction between these particles.  (Note: The GB potential has been used in 
modeling the phenyl units in a polystyrene simulation which claimed good 
results.  I note that there was a united atom representation for the CH and 
CH_2 units.)    

My C programming skills are minimal and so simplicity of new modifications is 
key.   Olaf suggested I take a closer look at the FENE  interaction but, after 
thinking it over, I believe there is an even simpler implementation.  The 
standard dihedral interaction is "part p_2 bond bondid p_1 p_3 p_4".  In this 
case p_1 and p_4 are needed for ascertaining the torsion angle across the 
bond.  If one made a conditional on the basis of "part p_2 bond bondid p_2 p_3 
p_3" then whenever the p_1 was set to p_2 or p_4 to p_3 the dihedral 
interaction subroutine could defer to the "dipole orientation" to ascertain 
the needed geometrical constraints.  Is there any reason this should/could not 
be done?

A secondary issue has to do with the subtracted LJ.  My guess is that there is 
no procedure to do the same with the Gay-Berne potential because this is the 
first go at linking GB particles within Espresso.  This all depends on whether 
the subtracted LJ subroutine has been coded to include any GB interactions.

I'm not sure I understand how mixtures of GB particles and spherical LJ 
particles are integrated.   

I also am not sure how the unit vectors u_i and u_j used in the GB interaction 
are established unless they refer back to the dipole orientation.  Am I 
missing something here?

Thanks, again, for any suggestions/feedback.


On Tuesday 13 October 2009 05:02:03 address@hidden 
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>    1. Re: Coarse Graining with a Gay Berne potential (Olaf Lenz)
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 12 Oct 2009 12:21:48 +0200
> From: Olaf Lenz <address@hidden>
> Subject: Re: [ESPResSo] Coarse Graining with a Gay Berne potential
> To: Michael Winokur <address@hidden>
> Cc: address@hidden
> Message-ID: <address@hidden>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 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
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> End of ESPResSo Digest, Vol 29, Issue 8
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Michael Winokur
Dept. of Physics, University of Wisconsin
1150 University Ave.
Madison, WI 53706
Phone: 608 263 7475 URL:

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