Version 1.0 Documentation

[skfegan]

Rewrite all the documentation to account for the code refactor.

This needs to be done before the next release, but should wait until most of the code changes are complete so that it accurately reflects the new code structure.

Issue #8 Amber inputs is one item that should go in the documentation.

[skfegan]

Document the choice of bin_width = 30. Argo's protein paper SI should have a good explanation.

[skfegan]

Document force_partitioning. Why is it used? When is it used? Why is the default value 0.5?

[skfegan]

Add to the documentation information about getting forces in the same trajectory file as the positions.

Also, comment on the amount of sampling needed to get reasonable results. Research question to determine how many frames you need. I expect it is proportional to the number of residues in the system. If the sampling is too small you get negative eigenvalues in the vibrational entropy calculation.