[gmx-users] Viscosity calculations

[Rini Gupta]

Dear Gromacs Users,

I am trying to learn viscosity calculations using non-equilibrium
method in Gromacs 4.5.4. I have gone through Hess paper and several
posts on viscosity calculation.
I have setup a system of pure water (32000 molecules) and run till 10 ns
using NPT and setting
cos-acceleration=0.1 nm/ps^2 in .mdp file.

Then, I have used following command to get viscosity from energy file.
g_energy_d -f .edr -s .tpr -o energy.xvg

and selected 1/viscosity from one of the options and I get,

Energy Average Err.Est. RMSD Tot-Drift
-----------------------------------------------------------------------
--------
1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg)

This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP

I have some doubts regarding this result:

1) Can anyone please tell me what are the units of viscosity here.
It shows from screen output (as well from energy.xvg) that 1/viscosity
is in m-s/kg units. But, the experimental value for pure water is 0.854
cP =0.000854 kg/m-s.
So, I have a doubt regarding units coming from GROMACS it is in cP or
kg/m-s as printed. If kg/ms are the units then, this value of viscosity
for pure water is not correct ?
Please tell me what I am doing wrong here.

2) Is this a right way of calculating viscosity using NEMD or I should
do it by using 2CosZ*Vel-X option. Please tell me how can I get
viscosity from this term.



Thanks and Regards,
Dr. Rini Gupta
UBC, Vancouver
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