On 2013-06-02 06:40, Marcelo Vanean wrote:
*On 2013-06-01 17:11, Marcelo Vanean wrote:
*
*On 2013-06-01 02:24, Marcelo Vanean wrote:
*
*Hello to everyone. In version 4.5.5, calculating the viscosity with the
command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a
value of zero for viscosity using the Einstein relation. Another question
in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas
in
version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way?
Evidently, there is an inconsistency in these different results. Help me,
please.
*
*I used the same energy file (ener.edr) and I get this results:
http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals.
*
*Maybe you can post the energy file on that site as well.
Have you tried to compute the pressure autocorrelation (using g_energy)?*
I didn't the pressure autocorrelation. A question: what does this analysis
tell me?
Check the equations in the manual and relevant literature. The viscosity
is computed from the pressure ACF.
I posted the energy file here:
http://www.4shared.com/file/SSAU1reN/ener.html.
That website does not work.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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