[gmx-users] ionic liquids - viscosity via green kubo relation

[Krzysztof Murzyn]

Hello,

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.

Regards,
km.


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 to
> calculate the viscosity of my liquid using the Green-Kubo relation.
>
> I have been calculating the Stress Autocorrelation Function (SACF) for Pxy
> using Matlab.  The autocorrelation window is 4 ps, and data was stored over
> a 1 ns production run every 5 fs (200 000 data points).  I know a 1 ns run
> 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 fact!).
>  Furthermore, when I integrate to compute the viscosity (I do not integrate
> the normalized curve obviously), I obtain around 6 cP which is 2 orders of
> 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?
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>