[gmx-users] g_dipole: dipole moment autocorrelation function

[Dommert Florian]

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.
> >>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se --
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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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