[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 


Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil

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