On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: > Dommert Florian skrev 2011-04-01 09.45: > > On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: > >> Hi, > >> I have a long-chain peptide which has a net charge of +5 . I was > >> wondering whether the g_dipole will give any reasonable dipole moment > >> for a molecule with a net charge. Is there any suggestion I should > >> follow regarding calculation of dipole-moment of a charged molecule . > >> I found that in the manual it is mentioned that 'For molecules with a > >> net charge, the net charge is subtracted atcenter of mass of the > >> molecule.'. I did not understand what it means. I am using > >> gromacs-4.0.7. > >> Sanku > >> > >> > > If you have a charged molecule the dipole moment is not unique, so you > > have to choose a reference point and this can be done by subtracting the > > net charge at this point. Write down the formula and rearange the terms > > and you will clearly see, what I mean. > > > > Cheers, > > Flo > > > And, if I recall correctly, there are two "natural" choices for this > reference pont. One is the center of charge, the other is the center of > mass. The latter is perhaps less intuitive, but better related to > experimental observables. >
If you choose the center of charge as reference point, then your molecular dipole moment will be zero, because the dipole moment for a charged molecule can be rewritten as: mu=qtot(x_coq-x_ref) /Flo > Erik > >> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> 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 gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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