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
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