On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: > On 2011-03-31 09.25, Dommert Florian wrote: > > On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: > >> On 2011-03-30 20.16, Nilesh Dhumal wrote: > >>> Thanks. > >>> How can I take average. > >> summing up and dividing by the number of sims. > >>> > >>> How much long I should run the simulation. > >> until the average converges. > >>> > >>> Nilesh > >>> > >>> On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: > >>>> On 2011-03-30 18.54, Nilesh Dhumal wrote: > >>>> > >>>>> Hello, > >>>>> > >>>>> > >>>>> I am trying to calculate the dipole moment autocorrelation > >>>>> function for my system (ionic liquid). I am using gromacs 4.0.7 version. > > > > Hello, > > > > I think you will get into some trouble when you try to calculate an > > autocorrelation function of property that is not continuous in time. In > > an ionic liquid you have contributions of the molecular dipole and > > contribution of the charged molecules to the dipole. The latter part is > > unfortunately not continuous due to jumping of the molecules over the > > PBCs. It depends what kind of property you want to calculate, but we > > experienced that simulations in the range of 50-100ns are required to > > reliably determine properties like the dielectric constant. The next > > point is that you have to save your coordinates and velocities quite > > often ( every 0.02ps we used) > > > > Check corresponding literature for further advice. > > Thanks Florian, for pointing that out. I forgot about it in my previous > mail. In order to compute the dielectric constant one could in principle > apply constant electric fields at different strengths and then > extrapolate to zero. Don't know whether that has been done. > >
In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo > > Cheers, > > > > Flo > >>>>> > >>>>> > >>>>> I run the simulation for 4 ns. I run the following command to > >>>>> calculate the dipole moment autocorrelation function > >>>>> > >>>>> g_dipoles -f water.trr -s water.tpr -corr total -c > >>>>> > >>>>> The function is not geting converge to zero. > >>>>> > >>>>> > >>>>> I want to use this data for calculation of power spectra by fourier > >>>>> transfom of dipole moment autocorrelation function. > >>>>> > >>>>> Can you tell why its not geting converge to zero? > >>>>> > >>>>> > >>>> You have to simulate at least a few 10s of ns for such slow liquids to > >>>> converge. Alternatively you can average over many independent simulations > >>>> (10s). > >>>> > >>>>> > >>>>> Thanks > >>>>> > >>>>> > >>>>> Nilesh > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Dept. of Cell& Molec. Biol., Uppsala University. > >>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > >>>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- > >>>> 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 > >>>> > >>>> > >>>> > >>> > >>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Dept. of Cell& Molec. Biol., Uppsala University. > >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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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-- 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