SimTk name change

This PR changes over a couple links.

Question: is `pandegroup/mdtraj` the right namespace for this project? This might be a good opportunity to register `mdtraj/mdtraj`. I'd like to continue to encourage more community involvement and contribution. E.g. with @kyleabeauchamp as a major force behind the project, contributions from @swails, @teng-lin, etc, it would be a shame if the naming of the project gave the wrong impression.