[gmx-users] Onsager coefficient

Tue Mar 31 17:03:21 CEST 2020

Den 2020-03-31 kl. 16:01, skrev Sina Omrani:
>   it is Maxwell-Stefan.
> 
> I want to calculate diffusion coefficients. from EMD we can calculate the
> MS diffusion coefficient that it is impossible to measure experimentally
> (because it is based on chemical potential gradient that is hard to
> measure) and with the thermodynamic correction factor it could be
> transformed into the Fick diffusion coefficient that is experimentally
> measurable. Although, there are NEMD method for calculating Fick diffusion
> coefficient but it is not prefered for some reasons.

OK, thanks, interesting. This does not look too promising:
https://en.wikipedia.org/wiki/Maxwell%E2%80%93Stefan_diffusion
"A major disadvantage of the Maxwell–Stefan theory is that the diffusion 
coefficients, with the exception of the diffusion of dilute gases, do 
not correspond to the Fick's diffusion coefficients and are therefore 
not tabulated."

Long time ago I published a paper about self-diffusion in alcohol-water 
mixtures as a function of concentration (J Chem Phys 119 (2003) p 7308). 
We mention "The relation between self diffusion and mutual diffusion is 
not straightforward58 and has hitherto only been studied by simulation 
for simple Lennard-Jones particles.59". But maybe this is not relevant 
at all.

> 
> On Tue, 31 Mar 2020 at 17:51, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
>> Den 2020-03-31 kl. 14:11, skrev Sina Omrani:
>>> As far as I know, the Onsager coefficient is used to calculate MS
>> diffusion
>>> coefficient that is a microscopic property. Then we can use this MS
>>> coefficient and relate it to macroscopic properties that we already have
>>> experimentally.
>>
>> What does MS mean?
>>
>> And for my curiosity, what kind of macroscopic properties are you after?
>> As far as I know many if not most macroscopic properties can be computed
>> directly from a simulation, but I may be wrong.
>>
>>
>>>
>>> On Tue, 31 Mar 2020 at 11:05, David van der Spoel <spoel at xray.bmc.uu.se>
>>> wrote:
>>>
>>>> Den 2020-03-31 kl. 08:17, skrev Dallas Warren:
>>>>> 3.5.9 Onsager Relations
>>>>> https://www.iue.tuwien.ac.at/phd/mwagner/node44.html
>>>>>
>>>>> See 3.146 and 3.147
>>>>
>>>> Thanks, I admit I am not familiar with this stuff, but seeing that this
>>>> falls under the heading "Macroscopic Transport Models", what is the
>>>> point in a microscopic simulation context? To prove or disprove or
>>>> compare to the analytical relations?
>>>>
>>>>>
>>>>> Catch ya,
>>>>>
>>>>> Dr. Dallas Warren
>>>>> Drug Delivery, Disposition and Dynamics
>>>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>>>> 381 Royal Parade, Parkville VIC 3052
>>>>> dallas.warren at monash.edu
>>>>> ---------------------------------
>>>>> When the only tool you own is a hammer, every problem begins to
>> resemble
>>>> a
>>>>> nail.
>>>>>
>>>>>
>>>>> On Tue, 31 Mar 2020 at 16:28, David van der Spoel <
>> spoel at xray.bmc.uu.se>
>>>>> wrote:
>>>>>
>>>>>> Den 2020-03-30 kl. 22:51, skrev Sina Omrani:
>>>>>>> Hi dear Gromacs users,
>>>>>>> Sorry to ask again but I really appreciate the help on this subject.
>>>>>>>
>>>>>>> thanks.
>>>>>>>
>>>>>>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani <sinaomrani96 at gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>>>      Hi, I would like to calculate the Onsager coefficient but after
>>>>>> months of
>>>>>>>> study, I'm not able to do that. if anybody can help me I would
>> really
>>>>>>>> appreciate it. I don't know if there is a specific command to do it
>> or
>>>>>> it
>>>>>>>> needs a series of analyses.
>>>>>>>>
>>>>>>>> P.S. I attached a picture of a formula that calculates the Onsager
>>>>>>>> coefficient from MD.
>>>>>>>>
>>>>>>>> sincerely,
>>>>>>>> Sina Omrani
>>>>>>>>
>>>>>> I see no attachment and google does not help either. What is an
>> Onsager
>>>>>> coefficient?
>>>>>>
>>>>>> --
>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>> http://www.icm.uu.se
>>>>>> --
>>>>>> Gromacs Users mailing list
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>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>> --
>>>> Gromacs Users mailing list
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>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se