[gmx-users] Shear viscosity

[Vitaly V. Chaban]

Hi all,

I am trying to master the art of shear viscosity calculation using
"g_energy -vis". Plotting the first column in visco.xvg over time, the
nearly straight line is obtained. Is it OK? How can one get the
viscosity value from these data? My simulation details for this task
are: NVT, 298K, shifted LJ with a big Rcut, PME, the substance is an
ionic liquid, simulation time is 2 ns with 1 fs timestep and every
10fs saving to ener.edr.

I suspect something is definitely wrong in my calculation of
viscosity. I tried the same procedure with SPC water (NPT, 1ns, PME,
shifted LJ) and got the complicated curve (in visco.xvg, first column)
with an average value of 0.55 cP. This result seems to be quite more
realistic as for me. Then what is the possible source of problem in my
above setup?

Thanks for any suggestions.
Vitaly