[gmx-users] Diffusion Coefficient from VAC

[Alexandre Suman de Araujo]

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
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>> 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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>
>
> -- 
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
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