[gmx-users] g_dipole: dipole moment autocorrelation function

[Dommert Florian]

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.

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


-- 
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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