[Pw_forum] Newbie Questions

Jack Shultz jackygrahamez at gmail.com
Mon Jan 7 19:40:14 CET 2008

Thank you Matteo.

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

I am getting help on babel, just having trouble with windows platform for
now. Easier than writing my own script to convert formats.

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.

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.

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?

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?

On Jan 7, 2008 12:50 PM, Matteo Cococcioni <matteo at umn.edu> wrote:

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