[gmx-users] Viscosity in PE

Esther Caballero-Manrique ecaballe at uoregon.edu
Thu Sep 7 17:03:27 CEST 2006

You can calculate it from the velocity autocorrelation function, which 
can be calculated using the g_velacc. The friction can be calculated 
from the integral of the velocity autocorrelation function 
(friction=3KbT/(integral of vacf)) and then the viscosity can be 
calculated using Stoke's equation (friction=6 x PI x visc x radius). But 
you need to have saved the velocities fairly often (say every 5 fs?). 
This came up recently in the mailing lists, you can search the velocity 
autocorrelation function. This method integrates the integral at time 
infinite (ie, see Morriss and Evan's book /Statistical Mechanics of 
Nonequilibrium Liquids, /now on the web @ 
http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or might 
not be a good approximation for your system. Otherwise you can do more 
sophisticated methods such as those outlined in chapter 6 of the manual.
Hope it helps,

Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR
Alessandro Mattozzi wrote:

> Dear Gromacs-users
> I have already run some MD, both in NVT and NPT, of Polyethylene (1000 
> atoms-backbone).
> I would like to estimate the viscosity of my systems. Is it possible 
> even if it is a rubbery solid? Which method is the most suitable?
> Regards
> Alessandro Mattozzi
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