<p>Hey Lin,</p>
<p>Did you consider PBC?<br>
Also, I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>> wrote:<br><br><br><div><br></div><div><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 face="arial, sans-serif"><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 face="arial, sans-serif"><span style="border-collapse:collapse">Here "A" are a string of atoms, most of them are carbons.</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">For the cis-structure</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">Dipole moment from GROMACS </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">Average = 33.0312</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">Std. Dev. = 3.5144</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">Error = 0.0236</span></font></div><div><span style="font-family:arial, sans-serif;border-collapse:collapse">Dipole moment from my calculation = 55.8675</span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="border-collapse:separate;font-family:arial"><div>
<font face="arial, sans-serif"><span style="border-collapse:collapse">For the trans-structure</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">Dipole moment from GROMACS </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">Average = 36.8470</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">Std. Dev. = 3.4917</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse">Error = 0.0238</span></font></div><div><span style="font-family:arial, sans-serif;border-collapse:collapse">Dipole moment from my calculation = 77.2346</span></div>
<div><span style="border-collapse:collapse"><br></span></div><div><span style="border-collapse:collapse"><br></span></div><div><span style="border-collapse:collapse"><br>
</span></div><div><span style="border-collapse:collapse">Questions:</span></div><div><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 style="border-collapse:collapse"> </span></div><div><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 style="border-collapse:collapse"><br></span></div><div><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 style="border-collapse:collapse"> </span></div><div><span style="border-collapse:collapse"><br></span></div></span></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br>Thank you<br><font color="#888888">Lin</font></span></div>
<br>--<br>
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