I want to brew 2.5 gallons of mead, since 5 gallons is a lot more than what I would need. Is using a 5 gallon glass jar ok? Or could this have negative affects on the mead?
For a primary fermentation that's fine. The headspace is of no consequence and you certainly won't have to worry about a Mead Eruption Accident (MEA). After fermentation is complete, you'll want to transfer it to a container without all that airspace during aging.
Size of fermentation container
Linear Mode
