[gmx-users] Viscosity by Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Sat Sep 8 08:34:06 CEST 2018

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.

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