Merge pull request #1 from juliebehr/liquids

subdirectories for output files; saving .pdb and .xml
Merge pull request #2 from juliebehr/liquids

generalized which force is nonbonded
Merge pull request #3 from juliebehr/liquids

Liquids
Merge pull request #4 from juliebehr/liquids

Production level number of steps
Merge pull request #5 from juliebehr/liquids

Check for file before writing
Merge remote-tracking branch 'upstream/liquids' into liquids