[Pw_forum] Newbie Questions

Matteo Cococcioni matteo at umn.edu
Mon Jan 7 18:50:15 CET 2008

Dear Jack,

I'm not sure I understand all of your questions. probably other people 
in the forum can help you more with some of them.

Jack Shultz wrote:
> Hello,
> I am new to Quantume Espresso and hope I can integrate it into my 
> distributed computing project as I decribe in this post 
> http://www.hydrogenathome.org/forum_thread.php?id=173 
> <http://www.hydrogenathome.org/forum_thread.php?id=173>
> As I am formulating my analytical methods, there may be flaws in what 
> I am proposing. I hope to use Climbing-Image Nudged Elastic Band 
> method to identify a transition state structure. Then use that 
> transition state structure in a molecular docking simulation. I then 
> run these simulations on metalic enzymes in hopes of identifing 
> optimal enzymes for water spliting hydrogen generating reactions. Of 
> course before I get that far I will run positve/negative controls to 
> QC my methods. Having resource sharing among volunteers through 
> Berkley's BOINC platform is really benefitial otherwise I would not 
> have the ability to do this kind of analysis on this scale.
> Anyway, my questions right now:
> 1) What output formats does QE support? I'm trying to get the command 
> line for open babel to convert xyz to other molecular formats and it 
> is giving me a hard time but if QE can output to PDB or MOL2 or other 
> molecular file format, I would really like to know how.

I'm not sure about the specific characteristic of these formats. As you 
probably know QE is well interfaced with XCrysDen and you may consider 
using this visualization program.

> 2) Are there command line tools that generate parameters for these 
> simulations like Exampl17? Where do I find them? I want to be able to 
> just supply a structure representing the substrate and another 
> representing the product of my reaction. I want to make these 
> parameters interchangeable because I am testing controls first. So I 
> would be able to test H2O2 binding to Catalase for instance.

It's not totally clear to me what you want to do here and what 
parameters you need. energy cut offs? lattice spacings? Many of them are 
determined by convergence. so I guess what you need is a script doing 
these convergences?

> 3) Finally, I don't know how to pose this question, perhaps I need 
> read more, how does one integrate DFT+U into models of reaction pathways?

In the paper PRL 97 103001 that Nicola Marzari has already suggested to 
you NEB was used with LDA+U. You don't need any integration: you just 
run an LDA+U calculation for every image.

Hope this is of some help.


> Thank you in advance for any assistance.
> Jack Shultz
> Project Leader http://hydrogenathome.org <http://hydrogenathome.org/>
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