[gmx-users] viscosity calculation using g_energy

[Ali Ahmed]

Any ideas?

On Thu, Apr 5, 2018 at 6:55 PM, Ali Ahmed <aa5635737 at gmail.com> wrote:

> Hello David,
> I have the same problem
> I run the simulation for 10 ns and I saved energies every 1 ps but the
> results were far and the curves go to negative values.
> Please, do have an idea how to get accurate results?
> Thank you
> Ali
>
>
>
>
> On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
>> Den 2018-04-05 kl. 09:19, skrev Jo:
>>
>>> Hello,
>>>
>>> I would like to calculate bulk and shear viscosity on gromacs using
>>> g_energy.  I have read a number of other emails about this topic but
>>> there
>>> still seems to be no conclusive answer to how to use this tool.  I use
>>> the
>>> following command:
>>>
>>> gmx energy -f  prod_500.edr -vis viscosity.xvg
>>>
>>
>> The einstein viscosity is usually more accurate. How long is your
>> simulation and how often do you save the energies?
>>
>>
>>> From this, a file called 'viscosity.xvg' is produced with data on time
>>>>
>>> (ps), shear viscosity, and bulk viscosity.  However, these values
>>> fluctuate
>>> wildly and are off from the correct viscosity for this model (SPCE) by at
>>> least an order of magnitude.  I know the simulation trajectory is correct
>>> as I have matched potential energy, density, and diffusion coefficition
>>> for
>>> these runs with literature.  However, the viscosity numbers are far off
>>> from the expected values.
>>>
>>> Any suggesions on what I can try?  I assume there must be a way to do it
>>> by
>>> hand via the pressure tensors.  Can someone directly me to how I can
>>> practically take the pressure tensors to calculate via Green-Kubo method
>>> the viscosity?
>>>
>>> Thanks,
>>>
>>> Shuwen
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>>
>> --
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>
>