<br><div>Hi</div><div><br></div><div>From David => </div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">"dipole is 48.0 sum of q_i x_i, therefore if you<br>
have large charge separation you will get a large dipole."</span></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">1. What does the coefficient 48.0 represent?</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">2. Is q_i = partial charge or charge on the atoms / united atoms?</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">3. Is x_i = the distance between the mass center of atom from the mass center of the molecule?</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">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? </span></font></div>
<div><br></div><div><br></div><div>Thank you</div><div>Lin</div><div><br></div><div><br></div><div><br></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 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>