Dommert Florian skrev 2011-04-01 09.45:
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole moment
for a molecule with a net charge. Is there any suggestion I should
follow regarding calculation of dipole-moment of a charged molecule .
I found that in the manual it is mentioned that 'For molecules with a
net charge, the net charge is subtracted atcenter of mass of the
molecule.'. I did not understand what it means. I am using
gromacs-4.0.7.
Sanku
If you have a charged molecule the dipole moment is not unique, so you
have to choose a reference point and this can be done by subtracting the
net charge at this point. Write down the formula and rearange the terms
and you will clearly see, what I mean.
Cheers,
Flo
And, if I recall correctly, there are two "natural" choices for this
reference pont. One is the center of charge, the other is the center of
mass. The latter is perhaps less intuitive, but better related to
experimental observables.
Erik
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