[CP2K:4571] BAND calculation with 16 frames

[Carlos Campana]

A bit more spice to Teo's main course,
One of the reasons why your calculation will have better chances of
succeeding when a TS candidate is provided
is because the band should display minimum lateral motion at the TS
(assuming not very stiff springs). The tension at the TS should help
stabilizing the band motion. As to the interpolation, it is a bit of a
guessing game that cannot be won without using your physical/chemical
intuition. Gradients (forces) in Cartesian coordinates tend to vary
abruptly from one point to another point in space. Thus, using collective
variables (when known) can help a lot to achieve convergence.
Carlos




On Wed, Aug 21, 2013 at 12:19 AM, Teodoro Laino <teodor... at gmail.com>wrote:

> Jörg,
>
> 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.
>
>
> Teo
>
> >
> > I hope that makes sense to you.
> >
> > All the best from London!
> >
> > Jörg
> > --
> > *************************************************************
> > Jörg Saßmannshausen
> > University College London
> > Department of Chemistry
> > Gordon Street
> > London
> > WC1H 0AJ
> >
> > 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
> >
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