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?
your problem is with definitions. This mu is only applice for simple
liquids and for the computation of the Kirkwood factor.
If you want to compute dielectric constant of peptides, then my best bet
would be to do the simulation at vaying water concentration
and then extrapolate to zero water concentration. You will have to do
very long simulations (5-10 ns) at each concentration to make it converge.
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?
Exactly according to those equations. Please check the source code in
gmx_dipoles.c
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
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--
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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