[gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

[Chih-Ying Lin]

Hi
According to the following website,

http://en.wikipedia.org/wiki/Bond_dipole_moment


[image: \mu = \delta \, d].
The bond dipole is modeled as +δ -- δ- with a distance *d* between the partial
charges <http://en.wikipedia.org/wiki/Partial_charges> +δ and δ-.
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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