[gmx-users] Non-equilibrium Viscosity Calculation

Yanmei Song ysong30 at asu.edu
Fri Apr 17 00:35:47 CEST 2009

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?

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

Yanmei Song
Department of Chemical Engineering

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