Newbie Questions

jackyg... at jackyg... at
Mon Jan 7 02:12:35 UTC 2008

I am looking at semi-empirical QM/MM as way to model catalyzed water
splitting hydrogen generating reactions. I've been veting this idea
among researchers and there seems to be problems with many of the
molecular modeling techniques such as QMC and DFT as applied to my
model. I am hoping to do this analysis over the internet through a
distributed computing platform called BOINC where volunteers donate
the idle times of their computers. I simply don't have the resources
to work on a super computer.

Here is more specifically what I am proposing. I hope to run this
analysis stochastically, perhaps treating the reaction in isolation,
going through different energy pathways, generating a different
transition state structures for each run along with associated free
energy profiles. Using the results of these reaction models, I will
run molecular docking analysis. So for a given reaction, we will have
generated a great quantity of data. We can thus compare the
theoretical vs the experimental, perhaps we can optimize these
simulations with heuristic algorithms.

If you have any advice or you can poke holes in my proposal, I welcome
hearing from you.  Or if you want to reply off list, you can reach me
at jackygrahamez at

I have just started installing the cp2k. If it is posible to build
this model with cp2k, I will really need help setting up these
simulations. I have not given up on DFT yet.


Jack Shultz
Project Leader

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