[CP2K:4570] BAND calculation with 16 frames
teodor... at gmail.com
Wed Aug 21 06:19:27 CEST 2013
On Aug 21, 2013, at 12:30 AM, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk> wrote:
> Dear all,
> 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 :) )
> 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?
> 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.
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.
> 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.
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.
> I hope that makes sense to you.
> All the best from London!
> Jörg Saßmannshausen
> University College London
> Department of Chemistry
> Gordon Street
> WC1H 0AJ
> email: j.sassma... at ucl.ac.uk
> web: http://sassy.formativ.net
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