These jupyer notebooks can be used to generate the figures in The ubiquity of
directional and reciprocating motions in enzymes out of equilibrium to be
published by Slochower and Gilson, 2017. There are two ways to interact with
this code: an interactive method and an automated method that can recreated the
published figures.
Assuming dihedral histograms have already been computed and the directories have
been specified in simulation.py, it is easy to inspect the behavior of a
single (or a few) dihedrals. If the histograms are unavailable, see below for
instructions on how to generate them and set the paths.
For example:
this = Simulation(data_source='adk_md_data')
this.name = 'chi2TYR103'
this.simulate()
plot_flux(this)perl script here. (This will require cpptraj)