Esther Caballero-Manrique wrote:
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
An alternative method that is implemented requires non-equibrium
simulations. Check out
@Article{Hess2002b,
author = {B. Hess},
title = {Determining the shear viscosity of model liquids from
molecular simulation},
journal = {J. Chem. Phys.},
year = 2002,
volume = 116,
pages = {209-217}
}
you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2
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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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