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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
