[CP2K:4571] BAND calculation with 16 frames

Jörg Saßmannshausen j.sassma... at ucl.ac.uk
Wed Aug 21 22:06:09 UTC 2013

Hi Theo,

thanks for the prompt reply!

> > I am in the process of setting up a BAND calculation with 16 frames.
> > Each frame got 82 atoms and if I recall it correctly I need to have the
> > cartesian coordinates in all frames in the same order. I assume that is
> > still correct? As this is a rather large molecule, doing it manually is
> > a bit
> correct - still, this should not be a limitation at all : during a geometry
> optimisation or during an MD, the coordinates are never swapped.. of
> course if you build your frames with different atoms order.. well.. then
> you are asking for trouble… (or at least for more additional work :) )

That was the question I had: how to build the frames from my DFT calculations 
to make sure the coordinates are not swapped when I set up the initial frames. 
Sorry if that was a bit confusing here.

> > cumbersome. I have tried to use GaussView for that but but it appears I
> > need a larger screen to get all 16 molecules in one window. :-(
> > Is there a better program to do that task?
> ?

See above.

> > Also, I want to investigate a dissociation reaction, i.e.:
> > 
> > A-B ---> A      B
> > 
> > Due to the flexibility of the molecules A and B, the forward reaction
> > might be different from the reverse reaction. Is there a way to
> > influence that when I am doing the BAND?
> A BAND is just a geometry optimisation is a wider space. What you put in,
> is what you will get out optimised… Rarely there is only one path
> connecting two points. This means that the success (in finding the minimum
> energy path) is entirely due to quality of the interpolating frames that
> you are feeding in.

True. I got that from Marcella's talk at the time and that was the reason why 
I done the DFT step-by-step calculations first, to get a good set of frames.

> Having said that, if you provide different frames for the opposite reaction
> you will get probably a different path - unless the landscape is
> relatively simple.

That is what I want to explore. I got some NMR data of that process and it 
would be nice to match that with some calculations, specially the energies 

> > I got the frames generated by pulling (pushing) A and B apart (together)
> > so I know the geometry is optimised here. I am doing steps of 0.3 A so
> > that should be ok as well (I hope). So, if I am using the optimised
> > geometries for the forward and reverse reaction I should be able to get
> > what I am expecting or is there something else which I need to bear in
> > mind?
> Just pulling apart the molecule and optimising them is quite risky:
> In the rare event that the reaction is only driven by this distance you
> will have automatically an optimised MEP. But, if the reaction is driven
> by much more complex reaction coordinates, then you are severely biasing
> the process. The best approach is to provide A, B and something similar to
> your TS (or any other crucial point, that you know is characterising your
> reaction). Let all other frames being interpolated and let the BAND
> optimisation relax the MEP.

Mh. I think I will make 3 runs then. 
It should be a very straightforward process though. Seeing where you are 
coming from, I think I don't need to provide all 16 frames here, 8 might be 
sufficient as well. I think I need to toy around here a bit but I get your 
general idea: apart from the start and end point just provide sufficient frames 
so you get a decent answer here.
Using a TS would be nice, but that is a bit tricky in my case. I will try that 
with the 3rd run, just to see where I am (which I might do first).
> Again, the final quality will be very much dependent on how good you'll be
> able to provide your TS (or these crucial intermediate points). If you do
> not have any idea about the TS, you can still try with a linear
> interpolation (or something similar to your procedure) and see what
> happens, analysing critically the results: most of the time it is easy to
> understand if you are just throwing ropes between minima, or you really
> got a MEP.


Many thanks for your help so far which is much appreciated!

All the best from London!


> Teo
> > I hope that makes sense to you.
> > 
> > All the best from London!
> > 
> > Jörg

Jörg Saßmannshausen
University College London
Department of Chemistry
Gordon Street

email: j.sassma... at ucl.ac.uk
web: http://sassy.formativ.net

Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

More information about the CP2K-user mailing list