[gmx-users] viscosity using green-kubo
Gmx QA
gmxquestions at gmail.com
Wed Dec 16 15:42:56 CET 2015
Dear gmx-users
I sent mail a couple days ago about viscosity calculations, but no-one
answered so maybe it was too lengthy, so better luck this time I hope.
I want to calculate viscosity using Green-Kubo formalism, and have run a
box with tip3p waters for 100 ps in NVE, saving data every 1 fs.
For green-kubo, I then first use gmx energy to get (one of) the
off-diagonal elements in the pressure tensor (Pxy in this case)
$ gmx energy -f nve_prod.edr -o nve_prod_pressure_tensor_pxy.xvg
Then, I use gmx analyze to calculate the auto-correlation function of the
Pxy pressure component
$ gmx analyze -f nve_prod_pressure_tensor_pxy.xvg -ac
nve_prod_pressure_tensor_pxy_acf.xvg -nonormalize
And then again gmx analyze to integrate it.
$ gmx analyze -f nve_prod_pressure_tensor_pxy_acf.xvg -integrate
That gives me :
Calculating the integral using the trapezium rule
Integral 1 1940.24341 +/- 0.00000
Which I then plug into the green-kubo formula
eta = V/(kB*T)* int(…) = …=
For my V=1.59e-26 m^3, T=303 K and with kB=1.38e-23 I get eta = 0.0074
Now, I am not sure about units, or about the validity of this answer. I
tried changing the unit of the pressure from bar to pascal by multiplying
with 100000, but the results makes equally less sense.
I have also read about averaging over several of the off-diagonal pressure
tensor components, which I could try, but is there anything fundamental
that I am missing above?
Hope for better luck with some answers this time!
/PK
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