Hi all, I am comparing viscosity calculation with eq md and non eq md. I want to calculate viscosity in eq md with green kubo equation. Can anyone suggest me how to get stress tensor from pressure tensor and its auto correction plot.
Thanks in advance. Regards, Shanu > On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN <vvcha...@gmail.com> wrote: > > EqMD methods work poorly for highly and moderate viscous liquids. > > > > > > > On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram <shanmugam...@gmail.com> > wrote: > >> I tried with g_energy -vis , but it calculates using einstein relation. I >> want to calculate using green kubo equation. >> >> >> regards, >> >> shanu >> >> On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel < >> sp...@xray.bmc.uu.se> >> wrote: >> >>>> On 11/01/16 22:54, shanmuga sundaram wrote: >>>> >>>> Hello all, >>>> >>>> >>>> I am trying to find viscosity using green kubo relation for Ionic >> Liquids. >>>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr. >>>> How >>>> to get stress autocorrelation function (SACF) from pressure >>>> autocorrelation >>>> function in MD simulations? Also how to change ACF windows (10, 50, >> 200ps) >>>> in getting autocorrelation function from gromacs (usually from g_analyze >>>> tool)? >>>> >>>> try >>> g_energy -vis >>> >>> >>>> regards, >>>> >>>> shanu >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
