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).

7 comments:

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.

http://avogadro.openmolecules.net/wiki/Hydrogen_Bond

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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