[gmx-users] Green Kubo viscocity calculation

[Aishwary Shivgan]

Currently I saving the energies after every 50 fs. Should I decrease more?
On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" <vvchaban at gmail.com> 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
> <aishwaryshivgan55 at gmail.com> 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 <vvchaban at gmail.com>
> > 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
> >> <aishwaryshivgan55 at gmail.com> 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
> >> > <spoel at xray.bmc.uu.se>
> >> > 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.
> >> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> >> >> --
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