I’m still not sure I understand your question. I think you’re asking, how does the random number generator re-seed between models?
The answer is, it doesn’t. The random number generator is not meddled with in any way between structures, in MPI mode or in normal mode. There’s no need to; so long as the different slave nodes started at different seeds, their random number trajectories will stay separate.
Another way to think of it is that the “seed” for subsequent models is just the last number produced from the last time the RNG was called for the previous model.
If you want to re-run just a particular MODEL from mid-trajectory (say, pdb_0245 out of 500), there’s no way to do that. The random number seed can help you figure out how to reproduce a trajectory, but there’s no reporting information to let you regenerate one single model. (This is not to say it isn’t possible – just that Rosetta doesn’t report the required information, and has no method for setting itself up in this fashion.)
Let me know if I’m still answering the wrong question.