[gmx-users] Viscosity calculations of gmx tcaf and gmx energy

[Mijiddorj B]

Dear GMX users,

I would like to discuss about the viscosity calculation of gromacs. From
the references, I found two different ways to find viscosity of solution
such as gmx tcaf and gmx energy methods.
I performed 1 ns simulation and saved the data every 10 fs. Then, I
extracted the viscosity using about two ways. The data were briefly
included in following parts.
If you have any experience, please advise me on how the calculations are
reliable and which method is more convenient in the literatures.

gmx tcaf gives following results
**********************
@    xaxis  label "k (nm\S-1\N)"
@    yaxis  label "\xh\f{} (10\S-3\N kg m\S-1\N s\S-1\N)"
@TYPE xy
 1.278 0.378769
...
2.213 0.286505
...
 2.556 0.276616
***************************

gmx energy gives several results
(a) Bulk viscosity
*****************************
@    title "Bulk Viscosity"
@    xaxis  label "Time (ps)"
@    yaxis  label "\xh\f{} (cp)"
@TYPE xy
@ s0 legend "Shear"
@ s1 legend "Bulk"
      0.01    0.273252    0.515646
      0.02    0.169156    0.692718
...
    499.98     1.42159  -0.0215052
    499.99     1.42339  -0.00296548
****************************
(b) Shear viscosity integral
****************************
@    title "Shear viscosity integral"
@    xaxis  label "Time (ps)"
@    yaxis  label "(kg m\S-1\N s\S-1\N ps)"
@TYPE xy
         0           0           0           0           0
      0.01  2.62525e-06  2.62677e-06  2.63998e-06  2.63067e-06
...
    249.99    0.198069    0.356375   0.0775561    0.210666
       250    0.198084    0.356393   0.0775584    0.210678
***********************************
(c) Shear viscosity using Einstein relation
**********
@    xaxis  label "Time (ps)"
@    yaxis  label "(kg m\S-1\N s\S-1\N)"
@TYPE xy
     0.005           0           0           0           0
     0.015  0.000262525  0.000262677  0.000263998  0.000263067
...
   249.995  0.00153552  0.00183501  0.000227655   0.0011994
   250.005   0.0015403  0.00183696  0.000226584  0.00120128
**********

Best regards,

Mijiddorj