[gmx-users] viscosity calculations

[Payman Pirzadeh]

Hello,

I am trying to calculate the viscosity of my pure water system at 275K. The
system has run for 40ns. I issued the following command:

 

g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis
sixsitewater_275K -b 0 -e 40000

 

The numbers I get in the output file are almost 100 times bigger than
reported literature. Am I doing something wrong or in the analysis procedure
sth is not divided properly?

Also, I tried to calculate the viscosity through the transverse current
autocorrelation function. The command I issued was:

 

g_tcaf_d_mpi -f 275K_50_50_50_2.trr -s 275K_50_50_50_2.tpr -oc
275K_50_50_50_2 -ov 275K_50_50_50_2 -mol -wt 5 -n watermolecules.ndx

 

The output is:

k  1.253  tau  2.383  eta  0.14641 10^-3 kg/(m s)

irow = 2, icol = 2

  2225392908111942225202360202531386163200.000      -0.195

       0.195       0.000

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  1.253  tau  1.000  eta  0.15845 10^-3 kg/(m s)

k  1.253  tau  0.133  eta  0.44011 10^-3 kg/(m s)

k  1.771  tau  0.455  eta  0.10514 10^-3 kg/(m s)

k  1.771  tau  1.458  eta  0.08329 10^-3 kg/(m s)

k  1.771  tau  0.348  eta  0.13366 10^-3 kg/(m s)

k  1.771  tau  0.324  eta  0.27031 10^-3 kg/(m s)

k  1.771  tau  0.320  eta  0.14002 10^-3 kg/(m s)

k  1.771  tau  2.100  eta  0.07649 10^-3 kg/(m s)

k  2.169  tau  1.541  eta  0.05321 10^-3 kg/(m s)

k  2.169  tau  2.201  eta  0.04949 10^-3 kg/(m s)

irow = 1, icol = 1

       0.000      -0.126

       0.126  708363867825344.750

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  2.169  tau  1.000  eta  0.05282 10^-3 kg/(m s)

k  2.169  tau  0.997  eta  0.07365 10^-3 kg/(m s)

k  2.505  tau  0.511  eta  0.05450 10^-3 kg/(m s)

irow = 1, icol = 1

       0.000       0.710

      -0.710  34533840121856978944.000

Numerical Recipes run-time error...

GAUSSJ: Singular Matrix-2

Fit failed!

k  2.505  tau  1.000  eta  0.03961 10^-3 kg/(m s)

k  2.505  tau  0.248  eta  0.06944 10^-3 kg/(m s)

Averaged over k-vectors:

k  1.253  tau  0.529  Omega  1.189  eta  0.35612 10^-3 kg/(m s)

k  1.771  tau  0.458  Omega  0.832  eta  0.14388 10^-3 kg/(m s)

k  2.169  tau  1.540  Omega  1.601  eta  0.05491 10^-3 kg/(m s)

k  2.505  tau  0.280  Omega  0.499  eta  0.07050 10^-3 kg/(m s)

 

I do not understand the failure parts of the output, also what should I do
with the output numbers?

I took a look at the -ov output. The final 4 numbers are not fittable on a
eta(k)=eta(0)*(1-ak^2). Am I fitting the wrong data?

Sorry for such a huge e-mail.

 

Paymon

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