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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
