[gmx-users] g_dipoles and charged molecules

Marc Baaden baaden at smplinux.de
Fri Nov 4 15:25:23 CET 2005


I have used g_dipoles to calculate the dipoles of several molecules (proteins)
in a simulation system. Results for one of these molecules are strange (10x
larger dipole than for the others although very similar in structure).

Furthermore I now realized that all those molecules are charged, the one
with the strange dipole positively the others negatively.
So I wonder how Gromacs calculates the dipoles for charged molecules ? As
far as I could find out, the dipole moment depends on the chosen origin
when a molecule is charged (not when it is neutral).

Am I right in guessing that Gromacs uses Sum over all atoms of atomic charge
times atom position vector with the current origin (eg bottom left corner of
a rectangular box I think) ? (formula taken from manual page 156)

Any general/enlightening comments on dipoles of charged molecules ?

Thanks in advance,
  Marc Baaden

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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