The control of the centroid/fullatom switch is protocol dependent. Each protocol has it’s own way of determining when to switch from centroid to full atom.
Most of the time it’s based off of cycle number. There’s a certain number of moves or cycles that happen in centroid mode, and when those are complete it switches over to the fullatom portion of the run. Some protocols will add protocol-specific filtering criteria to determine when a centroid structure is “good enough” to move on to fullatom.
OK. Is that number configurable? Surely “good enough” depends on (or is effected by) the number of residues? Or is it a calculated value with residue number a factor? Also are any other factors used in determining this threshold?