<div><br></div><div><br></div><div>Hi</div><div>According to the following website,</div><div><br></div><div><a href="http://en.wikipedia.org/wiki/Bond_dipole_moment">http://en.wikipedia.org/wiki/Bond_dipole_moment</a></div>
<div><br></div><div><font class="Apple-style-span" face="sans-serif"><span class="Apple-style-span" style="line-height: 19px;"><br></span></font></div><div><font class="Apple-style-span" face="sans-serif"><span class="Apple-style-span" style="line-height: 19px;"><span class="Apple-style-span" style="font-size: 13px; "><img class="tex" alt="\mu = \delta \, d" src="http://upload.wikimedia.org/math/7/8/b/78b632ee39700397e8df144f65503516.png" style="border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; vertical-align: middle; ">.</span></span></font></div>
<div><span class="Apple-style-span" style="font-family: sans-serif; font-size: 13px; line-height: 19px; ">The bond dipole is modeled as +ä — ä- with a distance <i>d</i> between the <a href="http://en.wikipedia.org/wiki/Partial_charges" title="Partial charges" class="mw-redirect" style="text-decoration: none; color: rgb(6, 69, 173); background-image: none; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: initial; background-position: initial initial; ">partial charges</a> +ä and ä-. </span></div>
<span class="Apple-style-span" style="font-family: sans-serif; font-size: 13px; line-height: 19px; ">For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments.</span><br>
<div><br></div><div><br></div><div>However, <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; ">for a molecule of multiple atoms,</span></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;">There may be more than one bond connected on one atom.</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;"> E</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;"> |</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;"> B - A - C</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;"> </span></font></div>
<div>partial charge of atom_A = -0.5 </div><div>partial charge of atom_B = 0.2</div><div>partial charge of atom_C = 0.35</div><div>partial charge of atom_E = 0.4</div><div><br></div><div><br></div><div><br></div><div>Which partial charges should I use when I calculate bond-dipole-moment of A-B ?</div>
<div>Which partial charges should I use when I calculate bond-dipole-moment of A-C ?</div><div>Which partial charges should I use when I calculate bond-dipole-moment of A-E ?</div><div><br></div><div>Thank you</div><div>Lin</div>
<div><br></div><div><br></div><div><br></div><div><br></div><div> </div><div><br></div><div><br></div><div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">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>> ></span></div>