[gmx-users] Viscosity calculations

Xiaohu Li xiaohuli914 at gmail.com
Mon Jan 17 07:10:05 CET 2011

   I'm trying to calculate viscosities of a few ionic liquid and has roughly
read about Hess's paper JCP 116 209, 2002.
Follows are the questions that I have
(1) For the method which uses the fluctuations of the pressure tensor using
Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis option and has
a few files such as evisco.xvg, eviscoi.xvg and visco.xvg
The evisco.xvg seems like the one I'm interested, since it has the title as
@    title "Shear viscosity using Einstein relation"
and the unit seems also correct. This file has 5 columns, if I understand it
correctly(by extrapolating from Hess's paper), the second to fourth columns
are the results from the off-diagonal elements of the pressure
tensor and the fifth one being the average. Hess's paper seems to be this
one(Figure 5). However, the results are way to low for the ionic liquid,
since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid.
the eviscoi.xvg file seems to be some kind of integral of evisco.xvg which
I'm not quite getting what it is.
visco.xvg contains the shear viscosity and bulk viscosity, which again seems
to be the one I'm looking for. However, the shear viscosity I'm looking
is(the region which roughly is constant) about 3~5 times higher than the
experiment. The simulation is 12ns long. Of course, this could mean (1) the
force field is bad or (2) the Green-kudo converges too slowly as Hess
pointed out.
Since it is not getting any useful result, I turned to non-equilibrium MD by
applying a shear external force, which is in (2)
(2) I tried both NVT and NPT simulations which uses berendsen coupling bath.
and set up the cos_acceleration = 0.1 nm/ps^2.
However, I tried to use g_energy -f *edr -s *tpr and by selecting
the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero data
points on all times.

I tried really hard on searching  results on the user list of gromacs but it
seems that there are quite a lot questions on this but not a single
satisfactory answer has been given, the most popular answer people gave is
refer to Hess's paper, but even though Hess was giving a good theoretical
background on this paper, practically on how to set up MD jobs is not
So I would appreciate anyone's hint.


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