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

Chih-Ying Lin chihying2008 at gmail.com
Thu Oct 21 07:01:44 CEST 2010

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

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
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