Till now I just set the bbox so that it would fit approximately twice the expected diameter of the whole complex, but your explanation is appealing, this parameter too might influence the result... I'll have a look at that.
You can also more directly influence by adding DiameterRestraints for the proteins.
By the way, trying to investigate the effect of the various parameters, I was wondering if there was any fancy debug mode that would store every intermediate configurations corresponding to the intermediate states occurring between the various MC and CG steps of the sampler procedure ? If not, I think I could just rewrite MonteCarloWithLocalOptimization::do_step() to insert intermediate configurations in a ConfigurationSet…
There are various such OptimizerStates that log every accepted step along the way. If you want to look at every evaluated step, you can use a misc.StateAdaptor to stick in OptimizerStates as ScoreStates (so they get called every time evaluate is called).