[CP2K:512] Newbie Questions

[Teodoro Laino]

Hi Jack,

On 7 Jan 2008, at 03:12, jackyg... at gmail.com wrote:

>
> 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.

The information you are giving on the model are so few that i would say
semi-empirical can be even worst in treating water hydrogen bonds  
compared
to DFT. Semi-empirical would be definitely faster but don't expect a  
realistic
representation of the HB pattern for your system (few people here  
have already
tried QMMM semi-empirical and can comment on that). Moreover the bond- 
breaking
energies.. I would be surprised to see numbers in better agreement  
than DFT.
Of course if you go for your own semi-empirical model, fully  
reparametrized for
your system the situation can be different.. but that's another story..

> 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.

Since I don't have more details on your project I can just give  
general comments:
In principle it should work..  BUT.. consider that the reaction on a  
smaller system
(what you call reaction in isolation) is mainly driven by the  
potential energy (the entropic
contribution can be very small). If you go on a larger system the  
entropic contribution
can be pretty large and you have no information on that since there  
are no data you
can extrapolate from your small cluster and your conclusions "could  
be" wrong.
So be careful in making your final conclusion in the logic chain  
(models/extrapolations
from cluster to larger systems).

> 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.

Which model?

cheers,
Teo