[gmx-users] Viscosity of water from gmx tcaf
gmxquestions at gmail.com
Wed Dec 16 09:11:26 CET 2015
No one that can comment on this? The very least on what data should be
fitted in visco_k.xvg to get the viscosity.
2015-12-15 10:14 GMT+01:00 Gmx QA <gmxquestions at gmail.com>:
> Dear users
> I am trying to teach myself how to calculate the viscosity of different
> simulations from gmx tcaf, and to that end I made a test system with a box
> of about 4000 water molecules, so that I can see if I can get a viscosity
> that matches that of water.
> I have read some mails on this list, and in particular the Berk Hess paper
> about various methods to calculate viscosity in gromacs, but I have some
> additional questions.
> From the help-text for gmx tcaf:
> The k-dependent viscosities in the -ov file should be fitted to eta(k) =
> (1 - a k^2) to obtain the viscosity at infinite wavelength.
> This is my command line for running gmx tcaf:
> $ gmx tcaf -f run.trr -s run.tpr -ov
> which gives me the visc_k.xvg file.
> I then tried to fit the data (per above) using xmgrace to y = a0 * (1 - a1
> * y * y), and get a0 = 0.41*10^-3 kg /m*s, which after unit conversion
> seems to be too low? (wikipedia says viscosity of water is 0.001 kg /m *s.
> On the other hand, gmx tcaf also says:
> When the box is cubic, one can use the option -oc, which averages the
> TCAFs over all k-vectors with the same length. This results in more
> accurate TCAFs. Both the cubic TCAFs and fits are written to -oc The cubic
> eta estimates are also written to -ov.
> Since I have a cubic box, I run
> $ gmx tcaf -f run.trr -s run.tpr -ov -oc
> which gives me another visc_k,xvg file with some (fitted?) data in it.
> What is this data?
> The following is also printed to stdout
> Averaged over k-vectors:
> k 1.273 tau 1.860 Omega 1.790 eta 0.14901 10^-3 kg/(m s)
> k 1.801 tau 1.133 Omega 2.061 eta 0.14087 10^-3 kg/(m s)
> k 2.206 tau 0.420 Omega 0.799 eta 0.09827 10^-3 kg/(m s)
> k 2.547 tau 0.340 Omega 0.599 eta 0.06810 10^-3 kg/(m s)
> Does gromacs somehow already compute the viscosity at "infinite
> wavelength"?, or am i missing something.
> I'd really, really appreciate some help here.
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