[CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule

[Michael Hale]

Great! Thank you. I'll look into those options and hopefully mess with it 
some more this weekend.

Is there much of a hobbyist community around computational chemistry? I'm a 
pretty experienced software developer, but still new to this. I know there 
are projects like Folding at Home which don't give you much control, and 
Chemistry Stack Exchange which is more just traditional Q&A. But I'd love 
to find community projects to help enhance digital chemistry textbooks with 
ab initio quantum MD animations of common reactions and such.

I actually first tried this during a weekend a couple of years ago. Here 
was the result:
https://www.youtube.com/watch?v=foG5LgFYb2o

I finally revisited it a week or two ago. I thought maybe just my initial 
conditions needed to be tweaked, but then I realized my simulation set up 
had deeper problems, haha. Thanks again for your help. I hope to post an 
update again soon. 

On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote:
>
> Hi 
>
> What I would do: 
>
> Small basis e.g. DZVP 
> LSD 
> SCF with Diagonalization and Broyden mixing, use all MOs 
> Fermi-Dirac Smearing with high temperature 
> NVT MD with velocity rescaling to get rid of excessive energy 
> Print CUBE file automatically during MD 
>
> regards 
>
> Juerg Hutter 
> -------------------------------------------------------------- 
> Juerg Hutter                         Phone : ++41 44 635 4491 
> Institut für Chemie C                FAX   : ++41 44 635 6838 
> Universität Zürich                   E-mail: h... at chem.uzh.ch 
> <javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zürich, Switzerland 
> --------------------------------------------------------------- 
>
> -----c... at googlegroups.com <javascript:> wrote: ----- 
> To: "cp2k" <c... at googlegroups.com <javascript:>> 
> From: "Michael Hale" 
> Sent by: c... at googlegroups.com <javascript:> 
> Date: 06/04/2020 05:08AM 
> Subject: [CP2K:13450] Visualize electron density during formation of a 
> water molecule 
>
> Hey, sorry for the basic question. I've skimmed some computational 
> chemistry books, but I still find the CP2K documentation a bit 
> overwhelming. I'm trying to put two hydrogens an an oxygen atom near each 
> other and watch the spontaneous assembly of a water molecule. I can make 
> the input file and have CP2K output the forces on the atoms and a cube file 
> that I can use to make a 3D visualization of the electron density in 
> Mathematica. Then I update the atom positions with a simple velocity Verlet 
> update and run CP2K again. The resulting animation looks how I want 
> stylistically, but the behavior is clearly not accurate. The atoms come 
> together and bounce off of each other and come back together and bounce off 
> harder. They keep getting more energy and bouncing farther and farther away 
> until they fly apart instead of bonding together. 
>
> Is the error that the energy calculation for the forces and electron 
> density isn't converging and causing the erratic behavior? Is the error 
> probably in the way I'm updating the atom positions manually? Can I use the 
> CP2K molecular dynamics functionality to do multiple steps of the 
> simulation at once while also outputting the cube file of the electron 
> density for each step? Is this type of simulation of the formation of small 
> molecules within the scope of CP2K? It seems most people typically assume 
> the molecules are already formed and they just want to simulate how those 
> molecules interact, not how atoms come together to form the small 
> molecules. 
>
> This is all just for fun. I just want to watch the animations and see how 
> "sticky" the atoms and molecules are. Thanks for any help and guidance you 
> might provide.   
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