Hi and thanks for sharing,
as pointed out earlier in this list, there is a published force field
for ILs to be used in gromacs. Maybe that would be a good starting point
for you, too. If I remember correct, they did not have the same ions,
but they had the most common ones.
I am not going to do any simulations with ILs, I'm just curious to see
the development around ILs.
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
[EMAIL PROTECTED]
SeungPyo Hong 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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
SeungPyo Hong wrote:
>
> On 8/16/07, *Mark Abraham* < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>> 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
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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
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
>
>
>
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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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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