# [gmx-users] Diffusion Coefficient from VAC

Wed Feb 22 20:57:42 CET 2006

```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> wrote:
>
> 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
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
>
>
>
>
> > 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>> 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>
> >     UIN: 6194055
> >     IFSC - USP - São Carlos - Brasil
> >
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> >
> > --
> > Old Dominion University, "VIRGINIA".
> >
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--
Old Dominion University, "VIRGINIA".
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