<br><div><br></div><div>Hi </div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">molecule dipole is 48.0 sum of q_i x_i</span></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">For <span class="Apple-style-span" style="border-collapse: separate; font-family: arial; ">a multiple-atoms molecule, the dipole moment of a covalent bond <span class="Apple-style-span" style="font-family: sans-serif; font-size: 13px; line-height: 19px; ">is a vector, parallel to the bond axis,</span></span></span></font></div>
<div>For a multiple-atoms molecule, which includes a ionic bond, <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">how to determine the direction of ionic bond dipole moment in theory ?</span></div>
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</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;">How does Gromacs determine <span class="Apple-style-span" style="font-size: 13px; ">the direction of ionic bond dipole moment ? </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px;"><br>
</span></font></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">Thank you</span></div>
<div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; white-space: pre; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; ">Lin</span></div>
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<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br>Try <a href="http://en.wikipedia.org/wiki/Electric_dipole_moment" target="_blank" style="color: rgb(0, 0, 204); ">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" style="color: rgb(0, 0, 204); ">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" style="color: rgb(0, 0, 204); ">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>></span></div>