Currently I saving the energies after every 50 fs. Should I decrease more? On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" <[email protected]> wrote:
> Sure, viscosity is overestimated, since you do not save pressure > components frequently enough to account for fast autocorrelations. > > > > > > On Tue, Sep 1, 2015 at 3:29 PM, Aishwary Shivgan > <[email protected]> wrote: > > 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]. > -- 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].
