[gmx-users] Non-equilibrium Viscosity Calculation

[David van der Spoel]

Yanmei Song wrote:
> 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?
At least equilibrium density.
> 
> 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
> acceleration."
You are interested (I assume) in the equilibrium viscosity, therefore 
you need to do this extrapolation. You can not assume that a small 
acceleration is small enough.
> 
> After I finish the run, what option I should use for g_energy in order
> to get the viscosity?
No option.

Just do it (tm).
> 
> 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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> 
> 
> 


-- 
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