<div>Thank you Matteo.</div>
<div> </div>
<div>Axel and I had number of correspondences and he gave me answers and his opinion on some my questions. I'm seeing the multiple challenges involved with a high throughput analysis for identifying catalysts based on molecular data.
</div>
<div> </div>
<div>I am getting help on babel, just having trouble with windows platform for now. Easier than writing my own script to convert formats.</div>
<div> </div>
<div>I am looking at different ways of combining estimates on transition state structures with molecular docking. Theoretically the transition state should be able to bind to the active site of an enzyme. I am going to look at computationally light methods that can run on a standard desktop at most three days. Perhaps something that gives similar but different transition state structures for each run. Starting off with simple catalysts and parameterizing these simulations.
</div>
<div> </div>
<div>NEB might not be the best approach within the confines of an entire enzyme due to the degrees of freedom. If studied in isolation it may yield inaccurate results due to missing entropy. Maybe it is close enough. Otherwise i could have substrate binding to the catalyst then only look at the 30 closest atoms near the binding site. Hopefully DFT plane-wave pseudo potentials are not too massive a computational task with that many atoms. I really just learning this stuff.
</div>
<div> </div>
<div>Or I can use semi-empirical QM/MM to do either of those types of experiments. At first I only plan to look at simple one step reactions. Either zero or first order. Would it be easier to analyze zero order or do those have a saddle point energy?
</div>
<div> </div>
<div>Anyway, I hear there are many theoretical problems with DFTs for the purpose I'm exploring. At the very least I hope to see what those problems are for my own edification. Where do I look for information on LDA+U calculations? Is it in journals that I have buy or is it posted somewhere?
</div>
<div> </div>
<div>Jack<br></div>
<div class="gmail_quote">On Jan 7, 2008 12:50 PM, Matteo Cococcioni <<a href="mailto:matteo@umn.edu">matteo@umn.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear Jack,<br><br>I'm not sure I understand all of your questions. probably other people<br>in the forum can help you more with some of them.
<br>
<div class="Ih2E3d"><br>Jack Shultz wrote:<br>> Hello,<br>><br>> I am new to Quantume Espresso and hope I can integrate it into my<br>> distributed computing project as I decribe in this post<br>> <a href="http://www.hydrogenathome.org/forum_thread.php?id=173" target="_blank">
http://www.hydrogenathome.org/forum_thread.php?id=173</a><br>> <<a href="http://www.hydrogenathome.org/forum_thread.php?id=173" target="_blank">http://www.hydrogenathome.org/forum_thread.php?id=173</a>><br>> As I am formulating my analytical methods, there may be flaws in what
<br>> I am proposing. I hope to use Climbing-Image Nudged Elastic Band<br>> method to identify a transition state structure. Then use that<br>> transition state structure in a molecular docking simulation. I then
<br>> run these simulations on metalic enzymes in hopes of identifing<br>> optimal enzymes for water spliting hydrogen generating reactions. Of<br>> course before I get that far I will run positve/negative controls to
<br>> QC my methods. Having resource sharing among volunteers through<br>> Berkley's BOINC platform is really benefitial otherwise I would not<br>> have the ability to do this kind of analysis on this scale.<br>
><br>> Anyway, my questions right now:<br>> 1) What output formats does QE support? I'm trying to get the command<br>> line for open babel to convert xyz to other molecular formats and it<br>> is giving me a hard time but if QE can output to PDB or MOL2 or other
<br>> molecular file format, I would really like to know how.<br>><br><br></div>I'm not sure about the specific characteristic of these formats. As you<br>probably know QE is well interfaced with XCrysDen and you may consider
<br>using this visualization program.<br>
<div class="Ih2E3d"><br>> 2) Are there command line tools that generate parameters for these<br>> simulations like Exampl17? Where do I find them? I want to be able to<br>> just supply a structure representing the substrate and another
<br>> representing the product of my reaction. I want to make these<br>> parameters interchangeable because I am testing controls first. So I<br>> would be able to test H2O2 binding to Catalase for instance.<br><br>
</div>It's not totally clear to me what you want to do here and what<br>parameters you need. energy cut offs? lattice spacings? Many of them are<br>determined by convergence. so I guess what you need is a script doing
<br>these convergences?<br>
<div class="Ih2E3d"><br>><br>> 3) Finally, I don't know how to pose this question, perhaps I need<br>> read more, how does one integrate DFT+U into models of reaction pathways?<br>><br><br></div>In the paper PRL 97 103001 that Nicola Marzari has already suggested to
<br>you NEB was used with LDA+U. You don't need any integration: you just<br>run an LDA+U calculation for every image.<br><br>Hope this is of some help.<br><br>Matteo<br>
<div class="Ih2E3d"><br><br><br>> Thank you in advance for any assistance.<br>><br>> Jack Shultz<br></div>> Project Leader <a href="http://hydrogenathome.org/" target="_blank">http://hydrogenathome.org</a> <
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