[gmx-users] Diffusion Coefficient from VAC
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Thu Feb 23 12:11:58 CET 2006
My calculations is for ions in water and I´m using the mass of the ions.
My units are correct, a think this is not my problem.
Thank´s
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil
Viswanadham Sridhara wrote:
> IF it is for pure water (bulk), then mass of the water should be
> m=(18e-3)/Ava, where Ava is the Avogadro number.
> KbT/m works out to be 1.3857e+005;
>
> On 2/22/06, * Alexandre Suman de Araujo* <asaraujo at if.sc.usp.br
> <mailto:asaraujo at if.sc.usp.br>> wrote:
>
> Yes, I tried and I had bad values too.
> I think the Kubo equation is to use in the non-normalized VAC,
> since the
> D = kT/M*integral is for normalized ones.
>
> Alexandre Suman de Araujo
> asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
>
>
>
> Viswanadham Sridhara wrote:
>
> > Did you try 1/3*your integral
> >
> > On 2/22/06, *Alexandre Suman de Araujo* < asaraujo at if.sc.usp.br
> <mailto:asaraujo at if.sc.usp.br>
> > <mailto:asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>>
> wrote:
> >
> > Hi Gmxers.
> >
> > I´m trying to calculate coefficient diffusion values for
> ions in
> > water.
> >
> > I made some calculations using MSD and the results were in good
> > agreement with experimental values.
> >
> > The problem is when I try to calculate it from integration
> of VAC
> > function for the ions, like in Rasaiah paper (J. Chem Phys.
> 101(8)
> > 6964).
> >
> > I made 40 simulations of 250 ps with 1 fs time step and
> output of
> > velocities every 1 fs. >From these simulations I calculated the
> > normalized VAC function from these 40 simulations and
> calculated the
> > mean. This methodology is implemented to have a good
> statistic and a
> > more smooth VAC function (without fluctuations that could
> make the
> > integral diverge). With this VAC function I use this equation to
> > calculate do diffusion coefficient:
> >
> > D = kT/M*Y, where Y is the integral of the VAC function
> >
> > The problem is that the value calculated from VAC does not
> agree with
> > one calculated from MSD.
> >
> > Does anyone knows any trick to perform this kind of calculation?
> > In the
> > paper cited above these two values are very near and I´m
> using the
> > same
> > methodology.
> >
> > Thank´s!
> >
> > --
> > Alexandre Suman de Araujo
> > asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> <mailto: asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>
> > UIN: 6194055
> > IFSC - USP - São Carlos - Brasil
> >
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> > --
> > Viswanadham Sridhara,
> > Graduate Research Assistant,
> > Old Dominion University, "VIRGINIA".
> >
> >------------------------------------------------------------------------
> >
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> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
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