[gmx-users] viscosity calculation using g_energy

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 5 21:12:39 CEST 2018

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.

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