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 formatting. /Erik > Thanks for supporting a confused student! > Guido > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
