[gmx-users] Non-equilibrium Viscosity Calculation

[David van der Spoel]

Yanmei Song wrote:
> Yes, I want to get the equilibrium viscosity. My question is how I can
> identify the system approach a zero acceleration after I try several
> values. Thank you so much for your help.
Plot viscosity as a function of acceleration. Check the reference 
(Wensink et al.) that I mailed earlier.
> 
> On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> 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
>> _______________________________________________
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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