On 2/19/19 4:03 AM, Andrea Graziadei wrote: > 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