On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote: > Interesting ... > > do you have a reference for this? >
Sure, a detailed discussion about charges for the liquid phase and results for molecular ionic liquids are published in: http://dx.doi.org/10.1039/C1FD00051A and http://pubs.acs.org/doi/abs/10.1021/ct200375v while the theory is based on: http://dx.doi.org/10.1063/1.3060164 and applied to water in: http://pubs.acs.org/doi/abs/10.1021/ct1002048 /Flo > XAvier. > > On May 14, 2012, at 12:01 PM, Dommert Florian wrote: > > > On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: > >> > >> > >> Hi, > >> > >> > >> You do not need to use the polarizable martini water model to > >> calculate the dipole of molecules. Or I am missing a point here! > >> > >> > >> g_dipole should do the work > >> > >> XAvier. > >> > > > > Hi, > > > > > > I want to point to another problem. If you simulate with a classical > > force field, you usually have an effective set of partial charges. > > This > > means polarization effects are often included in the partial charges. > > This in turn requires an appropriate calculation of the dipoles. A > > simple sum over the charges, like g_dipole or g_current does, is not > > sufficient. The true dipoles are only obtained, if the results from > > the > > MD are multiplied with a certain factor the is related to the > > high-frequency limit of the dielectric constant, the electronic > > dielectric constant. We have performed several studies on molecular > > ionic liquids and showed, that with a set of bulk charges, the dipole > > moments are reproduced correctly, if this electronic dielectric > > constant > > is taken into account appropriate. Also for water or any other > > molecule, > > the same arguments hold. For example, if TIP4P water is considered. > > Calculating the dielectric constant gives a value around 50, which is > > small compared to the exp. value of 80. However, if the correct > > dipoles > > are considered, a simulated value of around 80 is the result. Hence, > > it > > depends on the parametrization of the partial charges, how the dipole > > moment or any related property has to be calculated. > > > > If you are just interested in the static limit, an effective > > description > > with static partial charges is sufficient in my opinion. However, as > > soon as you are also interested in the time behavior, like the > > frequency > > spectrum of the dielectric constant or conductivity, you consider the > > electronic polarization explicitly with a corresponding force field, > > as > > Justin mentioned. > > > > > > Cheers, > > > > Flo > > > > > >> On May 13, 2012, at 15:11, dina dusti <dinadu...@yahoo.com> wrote: > >> > >> > >> > >>> Dear Justin, > >>> > >>> > >>> Thank you very much from your response. > >>> > >>> > >>> Best Regards > >>> Dina > >>> > >>> > >>> > >>> > >>> ____________________________________________________________________ > >>> > >>> From: Justin A. Lemkul <jalem...@vt.edu> > >>> To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS > >>> users <gmx-users@gromacs.org> > >>> Sent: Sunday, May 13, 2012 5:23 PM > >>> Subject: Re: [gmx-users] dipole moment > >>> > >>> > >>> > >>> > >>> On 5/13/12 8:41 AM, dina dusti wrote: > >>>> Dear GROMACS Specialists, > >>>> > >>>> I have one system consists of water and two other molecules. I > >>> work by MARTINI > >>>> CG force field. I want to calculate dipole moment of molecules in > >>> water. > >>>> May I ask you to help me, Please? > >>>> > >>> > >>> I doubt you can. Unless you are using version 2.P of the force > >>> field (which contains polarizable water), MARTINI uses a single, > >>> uncharged particle to represent water. If there are no charges, > >>> there is no dipole. > >>> > >>> -Justin > >>> > >>> -- ======================================== > >>> > >>> Justin A. Lemkul, Ph.D. > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> jalemkul[at]vt.edu | (540) 231-9080 > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >>> > >>> ======================================== > >>> > >>> > >>> > >>> -- > >>> 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 > >> -- > >> 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 > > -- > > 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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