[gmx-users] Viscosity in PE

Berk Hess gmx3 at hotmail.com
Fri Sep 8 08:34:16 CEST 2006

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at 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 
>>Hope it helps,
>An alternative method that is implemented requires non-equibrium 
>simulations. Check out
>   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.


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