[gmx-users] Viscosity by Gromacs

[Sam David]

Hello all,

I tried before to do viscosity calculations using GROMACS 5, with
npt ensemble. The results were so far from the experimental results. I did
a long simulation for toluene as an example and saved the trajectory every
1 ps but no results.
Have you gotten any results?
Sam

On Sat, Sep 8, 2018 at 1:34 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2018-09-07 kl. 13:22, skrev Tuanan Lourenço:
> > Hi everyone,
> >
> > I reading about the viscosity methods in the EMD by Gromacs and I have
> just
> > a simple question. In the user manual in section 6.11 there is an
> > explanation about the Einstein method used in the gmx energy -vis,
> however,
> > in the section 8.6.5 there is another explanation about the Green Kubo
> > method that is also implemented in gmx energy -vis.
> >
> > When I run the "gmx energy -vis" I have three outputs; evisco and eviscoi
> > (that are the Einstein viscosity and the integral respectively), enecorr
> > and visco. My question is about the visco.xvg file. Is in this file the
> > integration by Green Kubo correlation (equation 8.23 in gromacs manual).?
> > And the enercorr is just the ACF of the pressure tensor PXY (equation
> 8.22
> > in gromacs manual).
> >
> Yes this is correct.
>
> > Thank you very much,
> >
> > Cheers.
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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