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 [email protected] > > <mailto:[email protected]> > > 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 [email protected] > > 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 [email protected] > 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]
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