[gmx-users] viscosity calculation using g_energy

[Ali Ahmed]

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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