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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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