Assorted cleanup and installation standardization

[mattwthompson]

I changed a few of the notebooks to have a requirements.txt file that attempts to specify the packages needed to run it. With this changes, each notebook starts out with a conda install --file requirements.txt line. At best, it adds a couple seconds to a notebook. At worst, it should standardize what is need to run each notebook. Tagging #2

For the two notebooks that use GROMACS, I added a bash line that tries to find a gmx execuatable and, if that fails, installs it from conda. No need to have a duplicate install floating around, but it's better to grab from conda than not have at all or require a user build it themselves.

If these changes are popular, I can go through the other notebooks and unify them. I only did the GROMACS ones because I didn't want to install HOOMD-blue or GOMC on this machine.

I also included a couple other fixes so that things would actually run.

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