In finding out the viscosity of a system with non-equilibrium MD using GROMACS, an acceleration is given to the system due to which, the velocity profile changes. This change in energy is used to estimate viscosity as shown by the equations in this link.

For different molecular systems at the same T&P conditions and similar densities but with different acceleration amplitudes, the viscosity decreases with a different slope, as acceleration amplitude increases. As the viscosity at steady state is obtained by extrapolating these values to 0 acceleration amplitude, this slope is important in changing the values significantly. Therefore, I would like to know the property that this slope signifies.


1 Answer 1


This is shear thinning.

This kind of non-Newtonian behaviour is not really important for simple fluids like water at macroscopic scales, but it is readily observable in simulations of small systems on short timescales.

The physical reason for shear thinnning in water (at simulated timescales) is that water as a liquid has quite a complex structure where the molecules are interconnected in big hydrogen-bonded networks. These hydrogen bonds take a short while to develop (molecules have to reorient the right way to form a hydrogen bond), so the faster you shear, the less time the molecules have to grab onto their neighbors, the weaker the hydrogen bonding and thus the lower the viscosity.

The same occurs in solutions of polymers and the like, because their long chains get entangled if given enough time to do so. You won't see much shear thinning in nice simple fluids made of isotropic spheres like the Lennard-Jones fluid.

Apart from true shear thinning, you can also see artifacts due to inadequate thermostatting. Shearing the fluid injects a considerable amount of energy into the system. This can disturb energy equipartitioning between different degrees of freedom or make it difficult for the thermostat to hold the temperature constant. Viscosity depends a whole lot on temperature, so any temperature disturbance is going to affect the results. (This becomes a big problem when you go to excessively high shear rates.)

  • 1
    $\begingroup$ Nice answer but do you have a recommendation for a thermostat? I don't do viscosity measurements, but if I do, knowing ahead of time what is a good thermostat would be helpful $\endgroup$
    – Wesley
    Jan 25, 2022 at 17:28
  • $\begingroup$ @Wesley Nice follow-up question. I think this was a great first answer by TooTea and perhaps "What thermostat would your recommend for ____" could actually be a good question on the main site, where not only TooTea but anyone else could write up a helpful answer. $\endgroup$ Jan 25, 2022 at 21:16

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .