[gmx-users] g_dipole: dipole moment autocorrelation function

Thu Mar 31 15:12:51 CEST 2011

On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote: 
> Thanks Flo for detail reply.
> 
> Is it possible to put PBC off during calculation of dipole moment
> autocorrelation function.

No, thats the problem, because the volume of the system will increase
and dipole density will decrease, this not what you want. However I've
written the tool g_current, that allows to calculate the dielectric
constant and terms of which it is composed. Read our paper (DOI:
10.1063/1.3030948), which describes the procedure and look at the help,
what the programm can do.

Cheers,

Flo

> 
> 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.
> > SchrÃ¶der 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.
> >>>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se -- gmx-users
> >>>>>> mailing list    gmx-users at gromacs.org
> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>>>> Please search the archive at
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> >>>>>> posting! Please don't post (un)subscribe requests to the list.
> >>>>>> Use the
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> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> David van der Spoel, Ph.D., Professor of Biology
> >>>> Dept. of Cell&  Molec. Biol., Uppsala University.
> >>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> >>>> spoel at 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.
> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> >
> >
> > --
> > Florian Dommert
> > Dipl. - Phys.
> >
> >
> > Institute for Computational Physics
> > University Stuttgart
> >
> >
> > Pfaffenwaldring 27
> > 70569 Stuttgart
> >
> >
> > EMail: dommert at 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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> 
> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at 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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