# [gmx-users] Calculating shear viscosity using none-equilibrium MD: Viscosity dependent on acceleration magnitude

Florian Dommert dommert at icp.uni-stuttgart.de
Tue Jul 9 10:00:59 CEST 2013

```Hi,

I am not an expert in non-EQ MD, but a simulation time of 1ns for a
collective property in a honey-like substance like an IL sounds very short.
However, from my colleagues in the group of Prof. Müller-Plathe, who applied
non-EQ MD to derive viscosities, I heard that this method is quite reliable.
Take a look at their papers. As far as I can remember, the first authors of
the papers were Whei Zhao or Simon Butler.

/Flo

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Boning Wu
> Sent: Tuesday, July 09, 2013 3:00 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Calculating shear viscosity using none-equilibrium
MD:
> Viscosity dependent on acceleration magnitude
>
> Hi GMX Users,
>    I want to calculate the shear viscosity of an ionic liquid. Thus I
> applied the cos-acceleration in my box. However, I found that my
calculated
> viscosity got by "g_energy" is significantly dependent on magnitude of the
> acceleration. I don't know why. Even if this is a none-Newton liquid,why
> viscosity cannot converge at such a slow acceleration  My system consists
> of 216 ion pairs, and it has been equibrated under NPT for 5 ns. The box
> length is about 5 nm.
>
> *******
> Magnitude of the acceleration(nm/ps2)           Viscosity(cP)
> 0.01                                                         6102
> 0.03                                                         4452
> 0.06                                                         3580
> 0.1                                                           872
> 0.5                                                           48.5
> Experimental Value                                    85
> *******
> Here is my mdp file
>
> **************************************
> title                    = XXXX YYYY
> cpp                      = /lib/cpp
> define                   =
> integrator               = md
> dt                       = 0.001
> nsteps                   = 1000000
> nstxout                  = 50000
> nstvout                  = 50000
> nstlog                   = 50000
> nstenergy                = 100
> nstxtcout                = 5000
> xtc-grps                 = XXXX YYYY
> nstlist                  = 10
> ns-type                  = grid
> rlist                    = 1.5
> coulombtype              = PME
> rcoulomb                 = 1.5
> rvdw                     = 1.5
> tcoupl                   = Berendsen
> tc-grps                  = XXXX YYYY
> tau-t                    = 0.1 0.1
> ref-t                    = 298 298
> Pcoupl                   = NO
> ref-p                    = 1.0
> gen-vel                  = yes
> gen-temp                 = 298
> gen-seed                 = 173529
> constraints              = none
> cos-acceleration         = 0.5
> ***************************************
> Boning
>
> --
> Boning Wu
> Department of Chemistry and Chemical Biology
> Rutgers, the State University of New Jersey
> Piscataway, NJ, 08854
> boning.wu at rutgers.edu
> --
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```