Here are some wonderful programs that I use all the time in teaching and research (all programs are free and work on Windows, Mac, and LINUX):
I use Avogadro for building molecular structures and setting up input files for GAMESS (see below). Avogadro is still in beta version but quite close to "1.0" release. The main practical result of this is that there is very little documentation, and no real manual. Fortunately, Avogadro is very intuitive and there are a few screencasts that are quite informative (though I say so myself - some of them are mine).
I use GAMESS for quantum chemical calculations. It is not yet possible to submit GAMESS input files created in Avogadro automatically to the GAMESS program, so you must save the input file in Avogadro and submit the GAMESS job from the command line.
I visualize the GAMESS results by opening the output files in MacMolPlt (which also works on Windows, and LINUX despite its name). Much of what I do with MacMolPlt could also be done with Avogadro or Jmol (see below), but MacMolPlt is written specifically for GAMESS so it has some features lacking in the other two programs.
I usually do anything to do with structure in teaching with Jmol. Jmol is written in java, so the students can interact (rotate, zoom, download coordinates, etc.) with the models I post on the web. Furthermore, Jmol has a very powerful scripting language that allows one to create animations and control the animations via html. Note that virtually anytime you see a Jmol model on the web you have access to the coordinates by clicking on the window while holding down the ctrl key.
Finally, for anything to do with molecular dynamics I use Molecular Workbench in teaching. This wonderful program is molecular editor, MD engine, and analysis tool wrapped in one, and comes with a powerful scripting language. It is a bit like Avogadro/GAMESS/MacMolPlt/Jmol wrapped in one, but for MD instead of quantum chemistry. I'll show several examples of MW on this blog.
As you will see in future posts, I am a great fan of screencasts rather than written manuals and tutorials. Ironically, for screencasts I use a program that is neither free (it costs $100, ... ok $99) nor cross-platform (it works only on Macs running Leopard) called ScreenFlow. I am sure there are free alternatives, but based on what I read on google, this is by far the easiest to use. I can certainly testify that it is very easy to use.
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