[gmx-users] viscosity calculation using g_energy

Ali Ahmed aa5635737 at gmail.com
Fri Apr 6 01:55:06 CEST 2018

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

On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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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