[gmx-users] Ionic liquids

[SeungPyo Hong]

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
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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
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