[gmx-users] g_dipole ? => dipole moment ?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Oct 19 08:47:05 CEST 2010
On 2010-10-19 02.01, Chih-Ying Lin wrote:
> 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
> On 2010-10-18 03.30, Chih-Ying Lin wrote:
>> I confined one molecule in the center of box and issue the g_dipole
>> 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
> 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
>> 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
>> > 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
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