Krzysztof, 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 suggestion !!!
2013/5/7 Krzysztof Murzyn <krz...@gmail.com> > 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 <tomas...@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@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 > > > -- > 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 > -- 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
