[gmx-users] dipole moment

Mon May 14 12:48:43 CEST 2012

On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote: 
> Interesting ...
> 
> do you have a reference for this?
> 

Sure, a detailed discussion about charges for the liquid phase and
results for molecular ionic liquids are published in:

http://dx.doi.org/10.1039/C1FD00051A

and

http://pubs.acs.org/doi/abs/10.1021/ct200375v

while the theory is based on:

http://dx.doi.org/10.1063/1.3060164

and applied to water in:

http://pubs.acs.org/doi/abs/10.1021/ct1002048

/Flo

> XAvier.
> 
> On May 14, 2012, at 12:01 PM, Dommert Florian wrote:
> 
> > On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
> >>
> >>
> >> Hi,
> >>
> >>
> >> You do not need to use the polarizable martini water model to
> >> calculate the dipole of molecules. Or I am missing a point here!
> >>
> >>
> >> g_dipole should do the work
> >>
> >> XAvier.
> >>
> >
> > Hi,
> >
> >
> > I want to point to another problem. If you simulate with a classical
> > force field, you usually have an effective set of partial charges.  
> > This
> > means polarization effects are often included in the partial charges.
> > This in turn requires an appropriate calculation of the dipoles. A
> > simple sum over the charges, like g_dipole or g_current does, is not
> > sufficient. The true dipoles are only obtained, if the results from  
> > the
> > MD are multiplied with a certain factor the is related to the
> > high-frequency limit of the dielectric constant, the electronic
> > dielectric constant. We have performed several studies on molecular
> > ionic liquids and showed, that with a set of bulk charges, the dipole
> > moments are reproduced correctly, if this electronic dielectric  
> > constant
> > is taken into account appropriate. Also for water or any other  
> > molecule,
> > the same arguments hold. For example, if TIP4P water is considered.
> > Calculating the dielectric constant gives a value around 50, which is
> > small compared to the exp. value of 80. However, if the correct  
> > dipoles
> > are considered, a simulated value of around 80 is the result. Hence,  
> > it
> > depends on the parametrization of the partial charges, how the dipole
> > moment or any related property has to be calculated.
> >
> > If you are just interested in the static limit, an effective  
> > description
> > with static partial charges is sufficient in my opinion. However, as
> > soon as you are also interested in the time behavior, like the  
> > frequency
> > spectrum of the dielectric constant or conductivity, you consider the
> > electronic polarization explicitly with a corresponding force field,  
> > as
> > Justin mentioned.
> >
> >
> > Cheers,
> >
> > Flo
> >
> >
> >> On May 13, 2012, at 15:11, dina dusti <dinadusti at yahoo.com> wrote:
> >>
> >>
> >>
> >>> Dear Justin,
> >>>
> >>>
> >>> Thank you very much from your response.
> >>>
> >>>
> >>> Best Regards
> >>> Dina
> >>>
> >>>
> >>>
> >>>
> >>> ____________________________________________________________________
> >>>
> >>> From: Justin A. Lemkul <jalemkul at vt.edu>
> >>> To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS
> >>> users <gmx-users at gromacs.org>
> >>> Sent: Sunday, May 13, 2012 5:23 PM
> >>> Subject: Re: [gmx-users] dipole moment
> >>>
> >>>
> >>>
> >>>
> >>> On 5/13/12 8:41 AM, dina dusti wrote:
> >>>> Dear GROMACS Specialists,
> >>>>
> >>>> I have one system consists of water and two other molecules. I
> >>> work by MARTINI
> >>>> CG force field. I want to calculate dipole moment of molecules in
> >>> water.
> >>>> May I ask you to help me, Please?
> >>>>
> >>>
> >>> I doubt you can.  Unless you are using version 2.P of the force
> >>> field (which contains polarizable water), MARTINI uses a single,
> >>> uncharged particle to represent water.  If there are no charges,
> >>> there is no dipole.
> >>>
> >>> -Justin
> >>>
> >>> -- ========================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>
> >>> ========================================
> >>>
> >>>
> >>>
> >>> -- 
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> >
> > -- 
> > Florian Dommert
> > Dipl. - Phys.
> >
> > Institute for Computational Physics
> > University Stuttgart
> >
> > Pfaffenwaldring 27
> > 70569 Stuttgart
> >
> > EMail: dommert at icp.uni-stuttgart.de
> > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> >
> > Tel.: +49 - (0)711 - 68563613
> > Fax.: +49 - (0)711 - 68563658
> > -- 
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> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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