Thanks! I have another question, I have 1000 different runs and some of
them is better from others, is there a efficient way to choose only the
runs with the best scores?
and then use AnalysisReplicaExchange0 macro on a reduced list with the
best scores?
I don't think that will buy you anything - the clustering should do a
better job given the entire ensemble. If you want to discard entire
runs, you'd need to make that decision yourself. You can certainly set
the perfiltervalue though to quickly discard the worst-scoring models.