[gmx-users] Non-equilibrium Viscosity Calculation

[Yanmei Song]

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.

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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-- 
Yanmei Song
Department of Chemical Engineering
ASU