[gmx-users] Viscosity determination

[David van der Spoel]

On 1/8/10 1:59 AM, Lum Nforbi wrote:
> Dear all,
>
>    Below is my output for viscosity determination. In order to get a
> value for the viscosity, do I just take an average of the numbers in the
> third column?

In principle I think this is correct, but check the source code to make 
sure. You may also want to investigate NEMD methods (see Hess, JCP 116 
(2002) 209).

>
> # This file was created Wed Jan  6 16:25:24 2010
> # by the following command:
> # g_energy -f wfullmdrun_ener.edr -vis viscosity.xvg
> #
> # g_energy is part of G R O M A C S:
> #
> # Giant Rising Ordinary Mutants for A Clerical Setup
> #
> @    title "Bulk Viscosity"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "\8h\4 (cp)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Shear"
> @ s1 legend "Bulk"
>    0.199995    0.834084    0.546697
>     0.39999    0.883405     0.51992
>    0.599985    0.905292    0.495556
>     0.79998    0.913911    0.470734
>    0.999975    0.915144    0.452457
>     1.19997    0.915121    0.438746
>     1.39997    0.917106    0.430864
>     1.59996    0.920071    0.418252
>     1.79996    0.921777    0.403171
>     1.99995    0.918983    0.394725
>     2.19995    0.918122    0.387048
>     2.39994    0.923332    0.383686
>
> Thank you,
> Lum
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se