[gmx-users] Diffusion Coefficient from VAC
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Thu Feb 23 12:48:34 CET 2006
Ok, maybe I was not so clear.
My system is constituted by only one ion and water molecules (1400). I´m
trying to calculate de diffusion coefficient of this ion in water.
Using MSD the value is in relative good agreement with experiment (MSD =
1.5x10^-5 cm^2/s, experimental = 1.9 x10^-5 cm^2/s). Using VAC I have
the value of D = 0.9 x 10^-5 cm^2/s. The main problem is not the values
don´t agree very good with experimental but the values calculated from
VAC and MSD be so different, while in some papers that I read they are
very near.
The difference between the simulations I use to calculate MSD and VAC is
only the output time, where for MSD I have outputs every 200 fs while
for the VAC simulations the output is made every 1 fs. The models for
the water and ion are the same. The size of the box too.
I think my problem is in the way I´m integrating the VAC function. I´m
doing a simple integration and I believe that there is any details in
this calculation that I don´t know.
You said me something about multiply by cosine of the angular frequency
and scaling. Could you detail this procedure for me?
Thank you very much for your value help.
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil
Viswanadham Sridhara wrote:
> 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
> <mailto: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 <mailto: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>
> > <mailto: 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>
> <mailto: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>>
> > > <mailto: 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>>
> > <mailto: 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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