[gmx-users] Ways to calculate shear viscosity

[Jun Zhou]

Hi all,

I have sent this before but no one answers.

I want to simulate a couvette flow using gromacs by applying a deform
velocity at xz direction. For a pure water box, it works well though there
are warnings "the box is too skewed". When I put a surfactant micelle in
the middle, that warning still occurs and also terminates the simulation.
Does anyone have any suggestions about this?

Also, I read some paper they said they apply *the Lees–Edwards sliding
brick boundary conditions *to get a shear flow (10.1039/c7cp08349a), and
when I search the mailing list, Berk Hess also says he has a patch for
this.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-October/009325.html.
Can anyone show me how to do this?

Thanks.

-- 
*Jun ZHOU*
Postgraduate Student ,
Room 117, Building 36
Department of Civil Engineering,
Monash University,
Victoria 3800, Australia.