<br><br>HI<br><br>
dipole moment = 48.0 sum of q_i x_i<br>
x_i is the atomic position.<br>
The PBC is considered.<br><br><br>
I did not include the counter ion of the salt molecule in my calculation.<br>
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.<br>
Here "A" are a string of atoms, most of them are carbons.<br>
<br>
<br>
<br>
For the cis-structure<br>
Dipole moment from GROMACS<br>
Average = 33.0312<br>
Std. Dev. = 3.5144<br>
Error = 0.0236<br>
Dipole moment from my calculation = 55.8675<br>
<br>
<br>
<br>
For the trans-structure<br>
Dipole moment from GROMACS<br>
Average = 36.8470<br>
Std. Dev. = 3.4917<br>
Error = 0.0238<br>
Dipole moment from my calculation = 77.2346<br>
<br>
<br>
<br>
Questions:<br>
1. There is a huge discrepancy between my calculation results and GROMACS.<br>
Or, the two results are within acceptable discrepancy ???<br>
<br>
2. In the beginning, I suppose that the trans-structure has smaller dipole<br>
moment than cis-structure. However, it seems to be the opposite conclusion<br>
based on both GROMACS and my calculation. Is there something possible wrong<br>
???<br>
<br>
3. I get the partial charges from the Journal papers and the partial charges<br>
are derived for the similar molecules as mine. Is that wrong?<br>
<br>
<br>
<br>
<br>
Thank you<br>
Lin<br>
<br>
<br>
<br>
<br><br><br><br><br><br>Hey Lin,<br>
<br>
Did you consider PBC?<br>
Also, I wouldn't include the bromide if I were you, as it just adds noise,<br>
because it can move around freely. You seem to be interested in the change<br>
in dipole moment in the cation only, anyway.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>> wrote:<br>
<br>
<br>
<br>
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.<br>
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.<br>
Here "A" are a string of atoms, most of them are carbons.<br>
<br>
<br>
<br>
For the cis-structure<br>
Dipole moment from GROMACS<br>
Average = 33.0312<br>
Std. Dev. = 3.5144<br>
Error = 0.0236<br>
Dipole moment from my calculation = 55.8675<br>
<br>
<br>
<br>
For the trans-structure<br>
Dipole moment from GROMACS<br>
Average = 36.8470<br>
Std. Dev. = 3.4917<br>
Error = 0.0238<br>
Dipole moment from my calculation = 77.2346<br>
<br>
<br>
<br>
Questions:<br>
1. There is a huge discrepancy between my calculation results and GROMACS.<br>
Or, the two results are within acceptable discrepancy ???<br>
<br>
2. In the beginning, I suppose that the trans-structure has smaller dipole<br>
moment than cis-structure. However, it seems to be the opposite conclusion<br>
based on both GROMACS and my calculation. Is there something possible wrong<br>
???<br>
<br>
3. I get the partial charges from the Journal papers and the partial charges<br>
are derived for the similar molecules as mine. Is that wrong?<br>
<br>
<br>
<br>
<br>
Thank you<br>
Lin<br>
<br><br><br><br>