# [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

> 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:
>
>     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
>
>
>
>
>     > 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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