On Apr 18, 2012, at 9:10 PM, "Andrew DeYoung" <[email protected]> wrote:
> Dr. van der Spoel, > > Thank you for your time! So it seems that epsilon_r is just a "fudge > factor" and has nothing to do with the dielectric constant at the boundary > of the "PME/Ewald sphere." Is that dielectric constant actually > epsilon_surface? I am not very familiar at all with other MD codes, but a > colleague recently told me that some other codes use a default dielectric > constant of infinity at the surface. However, in Gromacs, the default value > of epsilon_surface is 0, which corresponds (I guess) to "no dielectric" at > the surface. Is this true? No, zero means in fact infinity and this is the default. Only for very special cases should you change this. > > Also, to complicate things further, I am using a pseudo 2-D PME summation > (ewald_geometry = 3dc). I have read in the manual entry for epsilon_surface > that epsilon_surface "does not affect the slab 3DC variant of the long range > corrections." If you have time, what does this mean? Does this mean that, > if I use ewald_geometry = 3dc, then there is "no dielectric" at the surface > (the medium surrounding the "Ewald sphere")? The 3dc only affects the dipole correction if I remember correctly. If you use it a refernce to a paper appears in your log file. > > Thank you! > > Andrew DeYoung > Carnegie Mellon University > >> epsilon_r should never be used with a regular force field because the >> balance between coulomb and other terms will be wrong. maybe we should >> remove the term. > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists
