[gmx-users] ionic liquids - viscosity via green kubo relation
tomasp04 at gmail.com
Sat May 18 10:28:28 CEST 2013
You were indeed correct to suggest augmenting the ACF window. For ionic
liquids, I have seen ACF windows that are around 500 ps, thank you for your
2013/5/7 Krzysztof Murzyn <krzymu at gmail.com>
> I would try to extend ACF window (10, 50, 200ps) but not too much since you
> might end with integrating noise which would lead to overestimation of
> viscosity. For water, 4ps seems to be ok but your liquid might have longer
> ACF tail so you are actually getting seriously underestimated viscosity.
> You should also run calculations for Pxz, Pyz, (Pxx-Pyy)/2 and (Pyy-Pzz)/2
> to improve statistics.
> On Tue, May 7, 2013 at 4:13 PM, Thomas P <tomasp04 at gmail.com> wrote:
> > Hello all,
> > I have a periodic system of composed of 200 pairs of
> > 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. I equilibrate
> > the system for 1.5 ns to the appropriate density under 1 atm and 300 K in
> > the NPT ensemble. As a sidenote, I do obtain the density cited in the
> > literature for the system and force field in question.
> > Once equilibrated, I pass into the NVE ensemble, and store the the Pxy
> > pressure tensor component of the entire group of atoms. I am doing this
> > calculate the viscosity of my liquid using the Green-Kubo relation.
> > I have been calculating the Stress Autocorrelation Function (SACF) for
> > using Matlab. The autocorrelation window is 4 ps, and data was stored
> > a 1 ns production run every 5 fs (200 000 data points). I know a 1 ns
> > may be slightly short for an ionic liquid, but the simulations take
> quite a
> > long time already, and I therefore wanted to rule out any other issues
> > before doing a longer run.
> > The SACF (normalized to 1) that I obtain is attached, and I do not really
> > know what to make of it; it is not smooth at all (quite jaggedy in
> > Furthermore, when I integrate to compute the viscosity (I do not
> > the normalized curve obviously), I obtain around 6 cP which is 2 orders
> > magnitude too small...
> > I am quite sure there are no errors in the parameters of my force field,
> > maybe someone can suggest something that I may have missed?
> > --
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