[gmx-users] g_dipoles and fluctuation of the total dipolemoment
humpert at caesar.de
Thu Aug 3 14:57:05 CEST 2006
Thanks for your responses and suggestions.
I think I understood the way epsilon is calculated in the source code,
although I'm not very fermiliar with C.
My question now is about your best bet of simulating the peptides in
different concentration of water.
What kind of simulation would be best in this case? My fist guess would
be a md with RF, as in the Gromacs paper (1998). Is it possible to
transfer the conditions of a system of water to a system of a peptide in
What's the difference between an extrapolation to zero water
concentration and the simulation of a peptide without water?
Thanks again for your help,
> 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
> > 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 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
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