Hello,
I am in the process of implementing some EM/crosslinking modelling using the PMI approach outlined in the tutorial for imp2.10.
I have managed to get my system up and running with PMI2, but I have a couple of very basic questions in regards to the ReplicaExchange0 class in PMI and the monte carlo sampler, as I do not really understand how ReplicaExchange is implemented in PMI.
Would it be possible for you to clarify how simulated annealing and monte carlo are implemented in the ReplicaExchange run in IMP, or point me towards the correct documentation?
Does the macro perform a number of simulated annealing and monte carlo steps at each ReplicaExchange frame? Or does this mean that if simulated annealing is enabled, it performs simulated annealing instead of simple monte carlo?
In general, what is the interplay between number_of_frames, monte_carlo_steps and simulated_annealing_minimum/maximum_temperature_nframes?
At the moment, I am running a single process (so no exchange is done, I think).
Additionally, I assume the weight of the restraints is constant throughout the run?
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?
I hope these questions make sense, as you see I am a bit confused..
Thank you very much in advance,
Andrea