What command should I use to do Cartesian or torsion-angle simulated annealing?
main.simulated_annealing=True will run Cartesian SA and main.simulated_annealing_torsion=True will torsion-angle SA. (You can set these in the .def/.eff file or add them to the command line.) You'll probably also want sites.individual="chain A" sites.torsion_angles="chain A" or similar.
simulated_annealing { start_temperature = 5000 ... }
These are the parameters for Cartesian SA. The torsion-angle SA parameters are in the tardy { mode = every_macro_cycle *second_and_before_last once first first_half ... } scope. Sorry it is a bit weird. It is for backward compatibility (for the 1.5-2 release). We are planning to revamp the parameters so it is more obvious how it works. Ralf