[gmx-users] g_dipole: dipole moment autocorrelation function

[Nilesh Dhumal]

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.
>>>>>> 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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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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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