[gmx-users] viscosity calculation using g_energy

Jo jojo412202 at gmail.com
Thu Apr 5 09:20:00 CEST 2018


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

>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?



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