<br><br>Hi<br>molecule dipole is 48.0 sum of q_i x_i<br><br>based on the following two websites, <br><i><b>x_i </b></i> is the <a href="http://en.wikipedia.org/wiki/Displacement_%28vector%29" title="Displacement (vector)">displacement vector</a> pointing from the negative charge to the positive charge. <br>
<br>what about the x_i for the salt-molecule, which dissociates into one counter ion and the rest of the molecule in water?<br><br><br><a href="http://en.wikipedia.org/wiki/Bond_dipole_moment">http://en.wikipedia.org/wiki/Bond_dipole_moment</a><br>
<a href="http://en.wikipedia.org/wiki/Electric_dipole_moment">http://en.wikipedia.org/wiki/Electric_dipole_moment</a><br><br><br>Thank you<br>Lin<br><br><br><br>On 2010-10-20 06.06, Chih-Ying Lin wrote:<br>
><br>
><br>
><br>
><br>
> Hi<br>
> molecule dipole is 48.0 sum of q_i x_i<br>
> x_i the bond length for covalent bond.<br>
<br>
No. x_i is the atomic position.<br>
<br>
> but what is "x_i" for salt-molecule?<br>
><br>
><br>
> For salt-molecule, the ionic bonds are broken in water solvent and the<br>
> counter ions are spread among the water.<br>
><br>
> What is the "x_i" of the ionic bond in the dipole moment calculation?<br>
> Is x_i equal to the distance of the two parts of the salt-molecules (the<br>
> counter ion and the rest of the molecule) even though the salt molecule<br>
> has dissolved in the water?<br>
><br>
> I mean, is x_i equal to the length of simulation box if the counter ion<br>
> and the rest of the molecule are in the two sides of the simulation box?<br>
><br>
><br>
> I mean, if Gromacs takes x_i as the length of simulation box if the<br>
> counter ion and the rest of the molecule are in the two sides of the<br>
> simulation box?<br>
><br>
> Thank you<br>
> Lin<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> Try <a href="http://en.wikipedia.org/wiki/Electric_dipole_moment" target="_blank">http://en.wikipedia.org/wiki/Electric_dipole_moment</a> , you might want<br>
> to read the part about calculating dipole moments for an array of point<br>
> charges, it is not difficult. 33 point charges are doable using pencil<br>
> and calculator in about 10min. Do not worry about the reference point as<br>
> long as your system is neutral, just set it to (0,0,0). Otherwise, take<br>
> any kind of first year physics book it will contain very similar<br>
> information.<br>
><br>
> On 10/19/2010 05:39 AM, Chih-Ying Lin wrote:<br>
>><br>
>><br>
>> Hi<br>
>> According to the following website,<br>
>><br>
>> <a href="http://en.wikipedia.org/wiki/Bond_dipole_moment" target="_blank">http://en.wikipedia.org/wiki/Bond_dipole_moment</a><br>
>><br>
>><br>
>> \mu = \delta \, d.<br>
>> The bond dipole is modeled as +ä -- ä- with a distance /d/ between the<br>
>> partial charges <<a href="http://en.wikipedia.org/wiki/Partial_charges" target="_blank">http://en.wikipedia.org/wiki/Partial_charges</a>> +ä and ä-.<br>
>> For a complete molecule the total molecular dipole moment may be<br>
>> approximated as the vector sum of individual bond dipole moments.<br>
>><br>
>><br>
>> However, for a molecule of multiple atoms,<br>
>> There may be more than one bond connected on one atom.<br>
>> E<br>
>> |<br>
>> B - A - C<br>
>> partial charge of atom_A = -0.5<br>
>> partial charge of atom_B = 0.2<br>
>> partial charge of atom_C = 0.35<br>
>> partial charge of atom_E = 0.4<br>
>><br>
>><br>
>><br>
>> Which partial charges should I use when I calculate bond-dipole-moment<br>
>> of A-B ?<br>
>> Which partial charges should I use when I calculate bond-dipole-moment<br>
>> of A-C ?<br>
>> Which partial charges should I use when I calculate bond-dipole-moment<br>
>> of A-E ?<br>
>><br>
>> Thank you<br>
>> Lin<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> On 2010-10-18 03.30, Chih-Ying Lin wrote:<br>
>> > HI<br>
>> > I confined one molecule in the center of box and issue the g_dipole<br>
>> command.<br>
>> > The average dipole moment is still around 32.<br>
>> > It is the molecule with 33 atoms / united atoms of most carbon groups,<br>
>> > isn't the dipole moment around 32 too high?<br>
>> > How can I test next and know that the dipole moment around 32 is<br>
>> > acceptable?<br>
>> By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you<br>
>> have large charge separation you will get a large dipole.<br>
>><br>
>> > Thank you<br>
>> > Lin<br>
>> > On 2010-10-16 21.36, Chih-Ying Lin wrote:<br>
>> > ><br>
>> > > Hi<br>
>> > > I issue the g_dipole command on Gromacs => And, the following<br>
>> > > information is shown.<br>
>> > > There are 10 molecules in the selection,<br>
>> > > Does the Average =32.1611 refer to the average for a single over the<br>
>> > > simulation time?<br>
>> > > Or, the Average = 32.1611 summing for all the 10 molecules over the<br>
>> > > simulation time?<br>
>> > > If the average = 32.1611 for a single molecule with 33 atoms / united<br>
>> > > atoms of most carbon groups, isn't the dipole moment too high?<br>
>> > I think this is the average per molecule. You may need to run trjconv<br>
>> > -pbc whole, because mdrun may break molecules in two parts, meaning that<br>
>> > the molecule becomes as big as the box.<br>
>> ><br>
>> > ><br>
>> > ><br>
>> > ><br>
>> > ><br>
>> > > What does "will subtract their charge at their center of mass" this<br>
>> > mean?<br>
>> > > Why "will subtract their charge at their center of mass" ?<br>
>> > ><br>
>> > ><br>
>> > ><br>
>><br>
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--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
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