[gmx-users] Green Kubo viscocity calculation

[Aishwary Shivgan]

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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