[gmx-users] Viscosity determination
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jan 8 08:59:39 CET 2010
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
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