<br><br>HI<br><br><br><span class="il">As Timo</span> M.D. <span class="il">Graen</span> described <br>"As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system."<br>
<br>On the other hand, I also play around the small salt-molecule as <span class="il">Timo</span> M.D. <span class="il">Graen</span> suggested.<br> "take two ions for a start, Na+ and Cl-, place<br>
them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for<br>
this system using different points of reference, i.e. (0,0,0) and<br>
(1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+<br>
ion to your system at NA(3,1,0) and repeat your calculation for the same<br>
reference points. "<br><br><br><br>So, i include the counter ion in my dipole moment-calculation this time.<br>But, the dipole moment of the system depends on where the counter ions are located.<br>For the cis-structure, the dipole moment is range from 45 to 75 as I randomly set the position of the counter ions.<br>
For the trans-structure, the dipole is range from 35 to 77 as I randomly set the position of the counter ions.<br><br><br><br>I have used GROMACS to test the dipole moment of the similar systems where GROMACS set the positions of the counter ions and the rest of molecules.<br>
For the cis-structure, the dipole moment is around 33. The standard deviation ~ 3<br>For the trans-structure, the dipole is around 36. The standard deviation ~ 3<br><br><br>How could GROMACS get the much lower standard deviation than what I calculated?<br>
Is there any specific rules while GROMACS decides the relative positions of the counter ions to the rest of the molecules? <br>My calculation result is not very close to what GROMACS derived.<br>Am I doing correctly ? <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 = 45 to 75<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 = range from 35 to 77<br><br><br><br><br>Thank you<br>Lin<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><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>