Sorry for late respond~ <br>I totally agree with you. <br>
Frankly, I don't have any idea about that kind of idea. <br>
I just help the guy to do what he want to do. <br>
Anyhow, as Mark said, I think some experiment is required to get a meaningful result. <br><br>First I warn you that this is not a good approach at all. <br>He want to simulate [EtNH3]+ [NO3]-. <br>I think that the structure of the is relatively simple and thus made their structure with WebMO(Gaussian).
<br>Then to get the groamcs topology, I use PRODRG server. <br>The partial charge of them are corrected to same as Gaussian result. <br><br>Then I placed them in a lattice with a same interval. <br>And run MD simulation with only solvent.
<br>By doing this I can get a solvent coordinate in a box. <br><br>Using this solvent coordinate and topology, you can run MD. <br>But PRODRG does not give an accurate information and thus be careful. <br><br>Good luck <br>
<br><div><span class="gmail_quote">On 8/16/07, <b class="gmail_sendername">Sampo Karkola</b> <<a href="mailto:sampo.karkola@helsinki.fi">sampo.karkola@helsinki.fi</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>nice to hear that someone else is also interested in doing MD in room<br>temperature ionic liquids. What kind of ions do you use? Bmim chlorides<br>perhaps, or do you have a larger counterion to bmim? Or a completely
<br>different cation? As Mark pointed out, if you do not have a properly<br>parameterised force field for ILs, the results probably are not<br>reliable, but I still would like to hear how did you define the<br>parameters and how the mdruns performed.
<br><br>Regards,<br><br>Sampo<br><br>______________________________<br>Sampo Karkola<br>Doctoral student<br><br>Laboratory of Organic Chemistry<br>Department of Chemistry<br>POBox 55, FIN-00014<br>University of Helsinki<br>
Finland<br><br>tel. +358 9 19150369<br>fax. +358 9 19150366<br><a href="mailto:sampo.karkola@helsinki.fi">sampo.karkola@helsinki.fi</a><br><br>SeungPyo Hong wrote:<br>><br>> On 8/16/07, *Mark Abraham* <<a href="mailto:Mark.Abraham@anu.edu.au">
Mark.Abraham@anu.edu.au</a><br>> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>> wrote:<br>><br>> Sampo Karkola wrote:<br>> > Dear all,<br>> ><br>
> > I was wondering if there are any parameters defined for ionic<br>> liquids?<br>> > Some enzymes have retained their activity when the solvent has been a<br>> > mixture of water and ionic liquids and it would be interesting to
<br>> study<br>> > the actual catalytical reactions in such a solvent.<br>><br>> I don't know how you can mix an ionic liquid and water and not get a<br>> really hot aqueous solution that would smash an enzyme :-)
<br>><br>> > I'm not an expert on the ionic liquids field or in simulating<br>> reactions,<br>> > but ionic liquids have been used in eg. microwave-assisted synthesis<br>> > with promising results. If one wants to study the reactions that take
<br>> > place in ionic liquids, with or without an enzyme catalysing it, are<br>> > there any well-known procedures to follow? Is Gromacs the correct<br>> tool<br>> > for that? I'm not going to study such reactions, at least not at the
<br>> > moment, but I'd just like to know how/if they can be done.<br>><br>> If you distort the solvent too far from pure water, the parameterization<br>> process of these force fields will no longer be valid for studying the
<br>> systems you want. Parameterizing new force fields for these solvents is<br>> probably not a worthwhile undertaking, and definitely not one to do<br>> lightly.<br>><br>> Mark<br>> _______________________________________________
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</a><br>><br>><br>> What a coincidence!<br>> A student in the biology major come to me he want to do simulation with<br>> ionic liquid.<br>> I have much doubt about that kind of simulation but becase he is eager
<br>> to do it.<br>> I try to make the solvent by placing the molecules in lattice and run MD<br>> under pressure coupling.<br>> Though I am also a beginner in this field, I am not sure of the<br>> plausiblity of this method but it seems to be OK to me.
<br>><br>> --<br>> --------------------------------------------------<br>> 'God used beautiful mathematics in creating the world.'<br>> -Paul Dirac<br>> 'But he created too many object.'<br>
> -Seungpyo Hong<br>><br>> Seungpyo Hong<br>> Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>> Tel. (82)-18-372-2468<br>> <a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr
</a> <mailto:<a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a>><br>> <a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a> <mailto:<a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>><br>>
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<br>'God used beautiful mathematics in creating the world.'<br>-Paul Dirac <br>'But he created too many objects.'<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>