Sunday, July 12, 2009

The AutoOpt tool in Avogadro

I am have been meaning to do a screencast of the Auto Optimization feature in Avogadro for a while. Fortunately Geoff Hutchison beat me to it, as you can see above, and did a much better job than I could have. To prove that point I made the screencast below. It shows how the autoopt tool can be used to illustrate intermolecular interactions - in this case hydrogen bonding between water molecules. Note how the H atoms on one water follow the O atom on the other when you move it (electrostatic attraction), how it's impossible to get the O atoms next to each other (electrostatic repulsion), and how one molecule gets out of the way when you try to push the other too close (steric repulsion).


Geoff said...

Ah, this was my next video, so you beat me to it.

One tip I'd give for the water/hydrogen-bonding exercise is to turn on the hydrogen bond display. It shows dashed lines which appear and disappear when h-bond interactions are formed or break.

BTW, how do you add the title screen to your screencasts?

Jan said...

I just tried that and that's a great tip. Thanks.

I use ScreenFlow, and just put a textbox in front of the movie. I can make a screencast of it if you are using ScreenFlow

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