[gmx-users] Ionic liquids
Jones de Andrade
johannesrs at gmail.com
Wed Aug 22 07:51:27 CEST 2007
Hi.
I would not agree with the fact that the approach isn't good.
The dialkylimidazolium cation class has a lot of interest on it, which
leaded to the development of force field for them rather than others.
It doesn't mean that there isn't force field for the [EtNH3]+ [NO3]- IL, but
means that there is no obvious reason for someone avoid those ions at a
first glance.
But, in fact, one should avoid the chlorine as counter-ion because it leads
to ILs with a slight larger melting point. There are better options.
On the other hand, a lot depends on the literature. I would expect that
there would be more studies for the interaction of enzimes with
dialkylimidazolium cation based ILs than any other class. BUT, I can be
deadly wrong on this point.
Back to the beggining: having 10 thousand water molecules, with 3 atoms only
and usually rigid, is much simpler than 10 thousand cations with about 25
atoms in a fully flexible structure, in a box which *must* have the same
number of countercharges, with anions of at least 5 atoms (which can
sometimes be made rigid). The computational cost of such a simulation would
rise in a amazingly way when compared to usual aqueous simulations.
Best regards and good luck!
Sincerally yours,
Jones
On 8/22/07, SeungPyo Hong <sp1020 at gmail.com> wrote:
>
> Sorry for late respond~
> I totally agree with you.
> Frankly, I don't have any idea about that kind of idea.
> I just help the guy to do what he want to do.
> Anyhow, as Mark said, I think some experiment is required to get a
> meaningful result.
>
> First I warn you that this is not a good approach at all.
> He want to simulate [EtNH3]+ [NO3]-.
> I think that the structure of the is relatively simple and thus made their
> structure with WebMO(Gaussian).
> Then to get the groamcs topology, I use PRODRG server.
> The partial charge of them are corrected to same as Gaussian result.
>
> Then I placed them in a lattice with a same interval.
> And run MD simulation with only solvent.
> By doing this I can get a solvent coordinate in a box.
>
> Using this solvent coordinate and topology, you can run MD.
> But PRODRG does not give an accurate information and thus be careful.
>
> Good luck
>
> On 8/16/07, Sampo Karkola <sampo.karkola at helsinki.fi> wrote:
> >
> > Hi,
> >
> > nice to hear that someone else is also interested in doing MD in room
> > temperature ionic liquids. What kind of ions do you use? Bmim chlorides
> > perhaps, or do you have a larger counterion to bmim? Or a completely
> > different cation? As Mark pointed out, if you do not have a properly
> > parameterised force field for ILs, the results probably are not
> > reliable, but I still would like to hear how did you define the
> > parameters and how the mdruns performed.
> >
> > Regards,
> >
> > Sampo
> >
> > ______________________________
> > Sampo Karkola
> > Doctoral student
> >
> > Laboratory of Organic Chemistry
> > Department of Chemistry
> > POBox 55, FIN-00014
> > University of Helsinki
> > Finland
> >
> > tel. +358 9 19150369
> > fax. +358 9 19150366
> > sampo.karkola at helsinki.fi
> >
> > SeungPyo Hong wrote:
> > >
> > > On 8/16/07, *Mark Abraham* < Mark.Abraham at anu.edu.au
> > > <mailto:Mark.Abraham at anu.edu.au>> wrote:
> > >
> > > Sampo Karkola wrote:
> > > > Dear all,
> > > >
> > > > I was wondering if there are any parameters defined for ionic
> > > liquids?
> > > > Some enzymes have retained their activity when the solvent has
> > been a
> > > > mixture of water and ionic liquids and it would be interesting
> > to
> > > study
> > > > the actual catalytical reactions in such a solvent.
> > >
> > > I don't know how you can mix an ionic liquid and water and not get
> > a
> > > really hot aqueous solution that would smash an enzyme :-)
> > >
> > > > I'm not an expert on the ionic liquids field or in simulating
> > > reactions,
> > > > but ionic liquids have been used in eg. microwave-assisted
> > synthesis
> > > > with promising results. If one wants to study the reactions
> > that take
> > > > place in ionic liquids, with or without an enzyme catalysing
> > it, are
> > > > there any well-known procedures to follow? Is Gromacs the
> > correct
> > > tool
> > > > for that? I'm not going to study such reactions, at least not
> > at the
> > > > moment, but I'd just like to know how/if they can be done.
> > >
> > > If you distort the solvent too far from pure water, the
> > parameterization
> > > process of these force fields will no longer be valid for studying
> > the
> > > systems you want. Parameterizing new force fields for these
> > solvents is
> > > probably not a worthwhile undertaking, and definitely not one to
> > do
> > > lightly.
> > >
> > > Mark
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > <mailto:gmx-users at gromacs.org>
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search
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> > >
> > >
> > > What a coincidence!
> > > A student in the biology major come to me he want to do simulation
> > with
> > > ionic liquid.
> > > I have much doubt about that kind of simulation but becase he is eager
> >
> > > to do it.
> > > I try to make the solvent by placing the molecules in lattice and run
> > MD
> > > under pressure coupling.
> > > Though I am also a beginner in this field, I am not sure of the
> > > plausiblity of this method but it seems to be OK to me.
> > >
> > > --
> > > --------------------------------------------------
> > > 'God used beautiful mathematics in creating the world.'
> > > -Paul Dirac
> > > 'But he created too many object.'
> > > -Seungpyo Hong
> > >
> > > Seungpyo Hong
> > > Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon
> > Korea
> > > Tel. (82)-18-372-2468
> > > sphong_ at kaist.ac.kr <mailto:sphong_ at kaist.ac.kr>
> > > sp1020 at gmail.com <mailto:sp1020 at gmail.com>
> > >
> > >
> > >
> > ------------------------------------------------------------------------
> > >
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>
>
>
> --
> --------------------------------------------------
> 'God used beautiful mathematics in creating the world.'
> -Paul Dirac
> 'But he created too many objects.'
> -Seungpyo Hong
>
> Seungpyo Hong
> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon
> Korea
> Tel. (82)-18-372-2468
> sphong_ at kaist.ac.kr
> sp1020 at gmail.com
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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