Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function.
I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: > 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 > -- > 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