[gmx-users] viscosity

David van der Spoel spoel at xray.bmc.uu.se
Sun Jun 2 06:01:44 CEST 2013

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)?

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

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