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
Esther Caballero-Manrique
Guenza Group
University of Oregon
Eugene, OR
usa
541-346-2485
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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