Friday, June 5, 2009

Some Jmol basics


Here is a Jmol application I wrote to illustrate rotational and vibrational energy states (in HCl) during a p-chem level lecture on energy states and statistical mechanics. You can find it here.

There are 3 main points:

1. It's an example of how you can use Jmol to visualize molecular motion. Maybe you like it and want to use it, or get inspired to do something much cooler.

2. The vibrational mode comes from a GAMESS calculation, and I show how you can access the GAMESS output file directly from Jmol. (Note you can get the coordinates of any molecule displayed with Jmol that you find on the web that way.)
November, 2010: In newer versions of Jmol the menu has changed a bit.  You now access the coordinates from "About" at the very bottom of the menu.

3. As with many web pages, the underlying html can be accessed from the browser.

So you have everything you need to reconstruct this example if you want. Of course you need to install Jmol on the computer that hosts the web site, and the GAMESS file needs be in the same directory as Jmol (at least on my web server).

The increases in rotational speed (100 and 1000) and vibrational displacements (0.1, 0.5, and 1.0) that I chose in the html code are completely arbitrary. I thought this got the point across. Click here for a complete list of commands.

A more complicated example (H2O) can be found here.
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