I'll add two sentences on related packages (i.e. emphasis on Python and trajectory analysis and reasonably well known and open source), including citations and links. The original MDA paper had an exhaustive survey but I'd do a short list including the following:
MDTools (original inspiration) and MMTK (granddaddy of all Python MD analysis packages) – sort of the historical background
I'll add two sentences on related packages (i.e. emphasis on Python and trajectory analysis and reasonably well known and open source), including citations and links. The original MDA paper had an exhaustive survey but I'd do a short list including the following: