[gmx-users] Diffusion Coefficient from VAC

Viswanadham Sridhara muta.mestri at gmail.com
Wed Feb 22 20:15:42 CET 2006

Did you try 1/3*your integral

On 2/22/06, Alexandre Suman de Araujo <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
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
> _______________________________________________
> 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/20060222/9defef82/attachment.html>

More information about the gromacs.org_gmx-users mailing list