In general, what is the interplay between number_of_frames,
monte_carlo_steps and
simulated_annealing_minimum/maximum_temperature_nframes?
number_of_frames is the number of output trajectory frames. Between each
frame, monte_carlo_steps of Monte Carlo are carried out. The simulated
annealing protocol is very simple (and I wouldn't use it - use REX
instead), just setting the Monte Carlo temperature alternately to the
minimum and maximum value for the given number of frames.
At the moment, I am running a single process (so no exchange is done, I
think).
Correct - the number of replicas is the number of processes.
Additionally, I assume the weight of the restraints is constant
throughout the run?
Sure, but the nuisances of any Bayesian restraints may be optimized.
Finally, I plan to implement multistate fitting. In this case, I would
have one set of crosslink restraints but the system present in multiple
conformations, with an EM density assigned to each state. I was
wondering how XL restraints are handled in this case? Is there an OR
statement applied?
Each state is (more or less) an independent copy of the system, so in
principle yes, each crosslink could be satisfied by either state.
Ben
--
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle