[gmx-users] viscosity

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se