[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

[Chih-Ying Lin]

HI

dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.
The PBC is considered.


I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346



Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

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
???

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?




Thank you
Lin









Hey Lin,

Did you consider PBC?
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.

Cheers,

Tsjerk

On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" <chihying2008 at gmail.com> wrote:



HI
dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.

I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.



For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675



For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346



Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

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
???

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?




Thank you
Lin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101021/e12d9726/attachment.html>