[gmx-users] g_dipole ? => dipole moment ?

[David van der Spoel]

On 2010-10-19 02.01, Chih-Ying Lin wrote:
>
> Hi
>
>  From David =>
> "dipole is 48.0 sum of q_i x_i, therefore if you
> have large charge separation you will get a large dipole."
>
>
> 1. What does the coefficient 48.0 represent?
Unit conversion from e nm to D.

> 2. Is q_i = partial charge or charge on the atoms / united atoms?
> 3. Is x_i = the distance between the mass center of atom from the mass
> center of the molecule?
> 4. What does the large charge separation mean?  Do you mean the charged
> molecule?  Or, Do you mean the molecule with a long carbon chain?
>

Please do a calculation on paper and you will understand.

>
> 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"  ?
>>  >
>>  >
>>  >
>


-- 
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