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

[Boning Wu]

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
***************************************
Thank you advance for your help!
Boning

-- 
Boning Wu
Graduate student
Department of Chemistry and Chemical Biology
Rutgers, the State University of New Jersey
Piscataway, NJ, 08854
boning.wu at rutgers.edu