[Pw_forum] Newbie Questions

Jack Shultz jackygrahamez at gmail.com
Sat Jan 5 17:59:41 CET 2008


I am new to Quantume Espresso and hope I can integrate it into my
distributed computing project as I decribe in this post
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.

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.

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?

Thank you in advance for any assistance.

Jack Shultz
Project Leader http://hydrogenathome.org
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