[gmx-users] Non-equilibrium Viscosity Calculation

Yanmei Song ysong30 at asu.edu
Mon Apr 20 18:36:43 CEST 2009

Dear David:

Thank you for your answer. i still have several questions.

Do I have to start the non-equilibrium simulation after the system
reach the equilibrium? Or I just need to start at the same starting
point as the my equilibrium systems?

What I need to do is just add the cos_acceleration: to the mdp file
and nothing else need to be changed, right?  Also what do you mean by
"You need to do a few values such that you can extrapolate to zero

After I finish the run, what option I should use for g_energy in order
to get the viscosity?

Thank you so much in advance!

On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
> 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.
> g_energy.
> 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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Yanmei Song
Department of Chemical Engineering

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