Batch Size Effects on Beer

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I am curious as to what problems could arise during fermentation in small batch sizes. I have three, three gallon carboys and am planning to split a six-gallon batch evenly between the three of them in order to experiment with more kinds of yeast. Is there anything that I should watch out for?
 
You should watch out for one of those little batches ending up being spectacular and then you are angry that you only have a half batch. Happens to me ALL the time!
 
Seems like having both tanks the same size is good. If you have a setup controlling temps in a freezer by taping the probe to your carboy etc, you may want to watch for temp differences between the two due to the different yeast strains?
 

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