[gmx-users] Diffusion Coefficient from VAC

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Feb 22 18:37:59 CET 2006

I mean that from MSD I have a value of 1.5 cm^2/s and from VAC 0.9 
cm^2/s. The experimental value is 1.9 cm^2/s.
In the paper I cited, they had values from VAC and MSD differing in 0.1 
cm^2/s in some cases.

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

Frederic Leroy 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!
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