[gmx-users] Diffusion Coefficient from VAC

[Viswanadham Sridhara]

Taking the integral of the velocity auto-correlation function multiplied by
cosine of the angular frequency and scaling it properly should give the
diffusion coefficient as a function of frequency.

On 2/22/06, Frederic Leroy <frederic.leroy at urv.net> wrote:
>
> What do you mean quantatively by "VAC does not agree with one calculated
> from MSD"?
>
>
>
> Alexandre Suman de Araujo 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!
> >
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060222/3372ee1c/attachment.html>