From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
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
In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.
But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.
Berk.
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