Add example to README.
Format README.
Modify README headings.
Modify README headings.
Remove mistake from README example.
Add Travis-CI build status image to the README.

One obtains this URL at https://travis-ci.org/simbody/simbody by clicking the
"Build Passing" image in the upper right. Except, this does not show up on my
computer. Probably because I'm not part of the simbody organization. So I'm not
completely sure this'll work.
Add some links to README.
Put travis build status on header line.
Add RNA GIF to README.
Fix RNA link.
Make the GIF a link to Simbios.
Change RNA link for when this is commit is merged into simbody/master.
Add theory manual link.
List other engines.
First complete draft of new README.
Fix spacing.
Merge pull request #110 from chrisdembia/readme

Descriptive README, addresses #108