[gmx-users] g_dipoles and fluctuation of the total dipole moment

[Guido Humpert]

Hello,

I want to use g_dipoles to calculate the dielectric constant epsilon of
peptides. The peptides contain between 20 and 40 Aminoacids and are
solvated in dodecahedron water box.
How can I define the -mu option in a system with a water solvated
peptid?
How is the total dipole moment calculated? I read the gromacs paper from
98 and there, a Clausius-Mosotti-type equation is used, but with the
fluctuation of the total dipole moment <M^2>. I read that the
fluctuation is kind of <M^2>-<M>^2 ? But how are those values calculated
properly?
In the online manual it's said that the aver.xvg file contains <|Mu|^2>
and < |Mu| >^2 and the fluctuation. But in the aver.xvg file it's
"<|M|\S2\N>", "<|M|>\S2\N" and "<|M|\S2\N> - <|M|>\S2\N". Why is there
only sometimes a \N and what does the \N mean? What's the right formula?
I tried a couple of different ways to calculate the fluctuation, but I
never got the same results as g_dipoles.

Thanks for supporting a confused student!
Guido