[gmx-users] Non-equilibrium Viscosity Calculation

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 17 08:33:55 CEST 2009

Yanmei Song wrote:
> Dear All:
> I wanted to get the viscosity of my simulated polymer system. From the
> manual it said that : GROMACS also has a non-equilibrium method for
> determining the viscosity" (page 123) Does this mean I just need to do
> a separate non-equilibrium MD run? In terms of mdp file, I just need
> to add the following options, right?
> acc_grps:
> accelerate:
> cos_acceleration:
Just the last one.

> My question is: first, how to set the value of cos_acceleration: ?

You need to do a few values such that you can extrapolate to zero 

> Second, after I finish the run, how can I get the viscosity from the
> simulation result? Anyone has done this yet? Thank you so much for
> your answer in advance.

J Chem Phys 116 (2002) 209-217
J Chem Phys 119 (2003) 7308-7317

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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