[gmx-users] g_dipoles and charged molecules

David spoel at xray.bmc.uu.se
Fri Nov 4 21:17:05 CET 2005

On Fri, 2005-11-04 at 15:25 +0100, Marc Baaden wrote:
> Hi,
> 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 ?
As was discussed on the CCL it is an ill defined problem. For proteins
one somewhat meaningful thing one could do is to find the isoelectric pH
(where the charge is 0) and determine the dipole there. An alternative
is to do a proper multipole expansion, see the book by Stone.
  author =       {A. J. Stone},
  title =        {The theory of intermolecular forces},
  publisher =    {Clarendon Press},
  year =         1996,
  address =      {Oxford}

> Thanks in advance,
>   Marc Baaden
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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