[gmx-users] dipole moment of a charged peptide

[Dommert Florian]

On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: 
> Dommert Florian skrev 2011-04-01 09.45:
> > On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
> >> Hi,
> >>     I have a long-chain peptide which has a net charge of  +5 . I was
> >> wondering whether the g_dipole will give any reasonable dipole moment
> >> for a molecule with a net charge. Is there any suggestion I should
> >> follow regarding calculation of dipole-moment of a charged molecule .
> >>   I found that in the manual it is mentioned that 'For molecules with a
> >> net charge, the net charge is subtracted atcenter of mass of the
> >> molecule.'.  I did not understand what it means. I am using
> >> gromacs-4.0.7.
> >> Sanku
> >>
> >>
> > If you have a charged molecule the dipole moment is not unique, so you
> > have to choose a reference point and this can be done by subtracting the
> > net charge at this point. Write down the formula and rearange the terms
> > and you will clearly see, what I mean.
> >
> > Cheers,
> > Flo
> >
> And, if I recall correctly, there are two "natural" choices for this 
> reference pont. One is the center of charge, the other is the center of 
> mass. The latter is perhaps less intuitive, but better related to 
> experimental observables.
> 

If you choose the center of charge as reference point, then your
molecular dipole moment will be zero, because the dipole moment for a
charged molecule can be rewritten as:

mu=qtot(x_coq-x_ref)

/Flo

> Erik
> >>
> >> -- 
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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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