[gmx-users] Diffusion Coefficient from VAC
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Wed Feb 22 16:46:39 CET 2006
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
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