[gmx-users] Onsager coefficient

Sina Omrani sinaomrani96 at gmail.com
Tue Mar 31 17:35:55 CEST 2020


Thanks, recently there have been studies that found a good match between MD
simulations and experimental results for multicomponent systems and shows
that there is a good chance for finding a relation for diffusion
coefficient as a function of concentration.
Self-diffusion coefficients can be used for predicting MS diffusion
coefficients (like Darken equation) but I don't want to use this kind of
relations. I am looking for the MS diffusion coefficient from MD to relate
it to Fick's coefficient in my ternary system.

On Tue, 31 Mar 2020 at 19:33, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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
> >>>> --
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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
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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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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