# [gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 20 08:34:03 CEST 2010

On 2010-10-20 06.06, Chih-Ying Lin wrote:
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>
>
>
> 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
>
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> 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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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se