[gmx-users] dipole moment

[XAvier Periole]

Interesting ...

do you have a reference for this?

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
>
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> Fax.: +49 - (0)711 - 68563658
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