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

Thomas P tomasp04 at gmail.com
Tue May 7 16:13:23 CEST 2013

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?

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