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

Erik Marklund erikm at xray.bmc.uu.se
Tue Aug 1 13:15:07 CEST 2006

On Tue, 2006-08-01 at 12:39 +0200, Guido Humpert wrote:
> 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.

Regarding the .xvg file: \S is a code used by (xm)grace for
superscripting, \S2 means writing the superscript '2'. \N is the grace
code for returning to normal text. In other words it's all just text


> Thanks for supporting a confused student!
> Guido
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Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se

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