Thanks, Do I need any special mdp options running the simulation? I tried g_energy -vis g_analyze -f visco.xvg it's giving me viscosities 10 times higher than actual.
On Sun, Aug 30, 2015 at 2:11 AM, Vitaly V. Chaban <[email protected]> wrote: > g_energy -vis > g_analyze -f visco.xvg > > > The method is handy only for systems with viscosity below 10 cP. > > > > > > On Sat, Aug 29, 2015 at 6:15 AM, Aishwary Shivgan > <[email protected]> wrote: > > Thank you David, > > It's not there in g_energy. I am currently calculating > polymer > > viscosity using transverse current autocorrelation function g_tcaf. I > just > > want to compare between the tcaf and green Kubo which is widely used for > > polymer viscosity calculation. > > > > On Sat, Aug 29, 2015 at 2:12 PM, David van der Spoel < > [email protected]> > > wrote: > > > >> On 29/08/15 10:19, Aishwary Shivgan wrote: > >> > >>> Hi gromacs users, > >>> Is there way to calculate viscosity from gromacs runs using > >>> green > >>> kubo formalism? > >>> > >>> Check g_energy. How accurate these are is hard to tell, but see e.g. > >> Hess, J Chem Phys 116 (2002) 209-217. > >> > >> I am working on implementing more methods to compute viscosity. > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Dept. of Cell & Molec. Biol., Uppsala University. > >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > >> [email protected] 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 [email protected]. > >> > > -- > > 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 [email protected]. > -- > 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 [email protected]. > -- 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 [email protected].
