[gmx-users] Viscosity in PE

[David van der Spoel]

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
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++