[gmx-users] Diffusion Coefficient from VAC
Viswanadham Sridhara
muta.mestri at gmail.com
Thu Feb 23 15:23:56 CET 2006
Can you give me some more details?
Are the ions just in bulk water?
Or are the ions going from bulk water through some protein and coming to
bulk water?
If you can explain me the situation, then people here can help you better.
I recently did some work in these lines too.
On 2/23/06, Alexandre Suman de Araujo <asaraujo at if.sc.usp.br> wrote:
>
> 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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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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