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 <[EMAIL PROTECTED]> 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]> 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] > > > > SeungPyo Hong wrote: > > > > > > On 8/16/07, *Mark Abraham* < [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 > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > <mailto:gmx-users@gromacs.org> > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search > > > < http://www.gromacs.org/search> before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > <mailto:[EMAIL PROTECTED]>. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > 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]> > > > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] . > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] . > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > -------------------------------------------------- > '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] > [EMAIL PROTECTED] > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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