Re: [gmx-users] ionic liquids - viscosity via green kubo relation
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 > 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 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] ionic liquids - viscosity via green kubo relation
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 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 listgmx-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 listgmx-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] ionic liquids - viscosity via green kubo relation
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 listgmx-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
