Thanx! Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden
-----Original Message----- From: [EMAIL PROTECTED] on behalf of Berk Hess Sent: Fri 9/8/2006 8:34 AM To: gmx-users@gromacs.org Subject: Re: [gmx-users] Viscosity in PE >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. _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<<winmail.dat>>
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
