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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