One way to deal with simulations that generate a lot of data that must be saved is to execute the simulation as a series of shorter runs, saving data at the end of each short run. For examples of how to do this see
Dealing with simulations that generate a lot of data
http://www.neuron.yale.edu/neuron/node/70
This and other useful tutorials and examples are available from links on NEURON's Documentation page
http://www.neuron.yale.edu/neuron/docs
