<br><div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">HI<br>dipole moment = 48.0 sum of q_i x_i<br>x_i is the atomic position.<br><br>I did not include the counter ion of the salt molecule in my calculation.</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Here "A" are a string of atoms, most of them are carbons.</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;"><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;">For the cis-structure</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Dipole moment from GROMACS </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Average = 33.0312</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Std. Dev. = 3.5144</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Error = 0.0236</span></font></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; ">Dipole moment from my calculation = 55.8675</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;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="border-collapse: separate; font-family: arial; "><div>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">For the trans-structure</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">Dipole moment from GROMACS </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">Average = 36.8470</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">Std. Dev. = 3.4917</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">Error = 0.0238</span></font></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; ">Dipole moment from my calculation = 77.2346</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">Questions:</span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ???</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> </span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ???</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse;">3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong?</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse;"> </span></div><div><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></div></span></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><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br>Thank you<br>Lin</span></div>