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

[Michael Hale]

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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