# [gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

Timo M.D. Graen tgraen at gwdg.de
Thu Oct 21 10:09:01 CEST 2010

reconsider your statement about the displacement vector. You should try
to understand the concepts of vectors and reference points first. It is
absolutely mandatory to do so before calculating dipole moments of
charged systems. It might also be wise to use a small test system to
practice on. For example take two ions for a start, Na+ and Cl-, place
them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for
this system using different points of reference, i.e. (0,0,0) and
(1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+
ion to your system at NA(3,1,0) and repeat your calculation for the same
reference points. What do you observe now? Also compare your results to
g_dipole for both systems. Are the results different in both cases? Now
think about the difficulties for calculating dipole moments for charged
molecules. The wikipedia sources you provided earlier should include all
information necessary to calculate the answers to this problem.

On 10/21/2010 12:35 AM, Chih-Ying Lin wrote:
>
>
> Hi
> molecule dipole is 48.0 sum of q_i x_i
>
> based on the following two websites,
> /*x_i */ is the displacement vector
> <http://en.wikipedia.org/wiki/Displacement_%28vector%29> pointing from
> the negative charge to the positive charge.
>
> what about the x_i for the salt-molecule, which dissociates into one
> counter ion and the rest of the molecule in water?
>
>
> http://en.wikipedia.org/wiki/Bond_dipole_moment
> http://en.wikipedia.org/wiki/Electric_dipole_moment
>
>
> Thank you
> Lin
>
>
>
> On 2010-10-20 06.06, Chih-Ying Lin wrote:
>  >
>  >
>  >
>  >
>  > Hi
>  > molecule dipole is 48.0 sum of q_i x_i
>  > x_i the bond length for covalent bond.
>
> No. x_i is the atomic position.
>
>  > but what is "x_i" for salt-molecule?
>  >
>  >
>  > For salt-molecule, the ionic bonds are broken in water solvent and the
>  > counter ions are spread among the water.
>  >
>  > What is the "x_i" of the ionic bond in the dipole moment calculation?
>  > Is x_i equal to the distance of the two parts of the salt-molecules (the
>  > counter ion and the rest of the molecule) even though the salt molecule
>  > has dissolved in the water?
>  >
>  > I mean, is x_i equal to the length of simulation box if the counter ion
>  > and the rest of the molecule are in the two sides of the simulation box?
>  >
>  >
>  > I mean, if Gromacs takes x_i as the length of simulation box if the
>  > counter ion and the rest of the molecule are in the two sides of the
>  > simulation box?
>  >
>  > Thank you
>  > Lin
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  > Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
>  > to read the part about calculating dipole moments for an array of point
>  > charges, it is not difficult. 33 point charges are doable using pencil
>  > and calculator in about 10min. Do not worry about the reference point as
>  > long as your system is neutral, just set it to (0,0,0). Otherwise, take
>  > any kind of first year physics book it will contain very similar
>  > information.
>  >
>  > On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:
>  >>
>  >>
>  >>  Hi
>  >>  According to the following website,
>  >>
>  >> http://en.wikipedia.org/wiki/Bond_dipole_moment
>  >>
>  >>
>  >>  \mu = \delta \, d.
>  >>  The bond dipole is modeled as +ä -- ä- with a distance /d/ between the
>  >>  partial charges <http://en.wikipedia.org/wiki/Partial_charges> +ä
> and ä-.
>  >>  For a complete molecule the total molecular dipole moment may be
>  >>  approximated as the vector sum of individual bond dipole moments.
>  >>
>  >>
>  >>  However, for a molecule of multiple atoms,
>  >>  There may be more than one bond connected on one atom.
>  >>  E
>  >>  |
>  >>  B - A - C
>  >>  partial charge of atom_A = -0.5
>  >>  partial charge of atom_B = 0.2
>  >>  partial charge of atom_C = 0.35
>  >>  partial charge of atom_E = 0.4
>  >>
>  >>
>  >>
>  >>  Which partial charges should I use when I calculate bond-dipole-moment
>  >>  of A-B ?
>  >>  Which partial charges should I use when I calculate bond-dipole-moment
>  >>  of A-C ?
>  >>  Which partial charges should I use when I calculate bond-dipole-moment
>  >>  of A-E ?
>  >>
>  >>  Thank you
>  >>  Lin
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>  On 2010-10-18 03.30, Chih-Ying Lin wrote:
>  >> >  HI
>  >> >  I confined one molecule in the center of box and issue the g_dipole
>  >>  command.
>  >> >  The average dipole moment is still around 32.
>  >> >  It is the molecule with 33 atoms / united atoms of most carbon
> groups,
>  >> >  isn't the dipole moment around 32 too high?
>  >> >  How can I test next and know that the dipole moment around 32 is
>  >> >  acceptable?
>  >>  By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore
> if you
>  >>  have large charge separation you will get a large dipole.
>  >>
>  >> >  Thank you
>  >> >  Lin
>  >> >  On 2010-10-16 21.36, Chih-Ying Lin wrote:
>  >> > >
>  >> > > Hi
>  >> > > I issue the g_dipole command on Gromacs => And, the following
>  >> > > information is shown.
>  >> > > There are 10 molecules in the selection,
>  >> > > Does the Average =32.1611 refer to the average for a single over the
>  >> > > simulation time?
>  >> > > Or, the Average = 32.1611 summing for all the 10 molecules over the
>  >> > > simulation time?
>  >> > > If the average = 32.1611 for a single molecule with 33 atoms /
> united
>  >> > > atoms of most carbon groups, isn't the dipole moment too high?
>  >> >  I think this is the average per molecule. You may need to run trjconv
>  >> >  -pbc whole, because mdrun may break molecules in two parts,
> meaning that
>  >> >  the molecule becomes as big as the box.
>  >> >
>  >> > >
>  >> > >
>  >> > >
>  >> > >
>  >> > > What does "will subtract their charge at their center of mass" this
>  >> >  mean?
>  >> > > Why "will subtract their charge at their center of mass" ?
>  >> > >
>  >> > >
>  >> > >
>  >>
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> Dept. of Cell & Molec. Biol., Uppsala University.
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--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Computational Biomolecular Chemistry Group,
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgraen at gwdg.de