The infamous double post.... Asked in Newsgroup and answered. Try parfor in the parallel toolbox. If your computer has multicores, you can run 2+ simulations at the same time.
Just as a follow up, how long does running ODE45 take? Are we talking seconds or minutes?
Is your function large? I run a simulation with ~3000 odes, using ode15s and this takes between 100-1000 seconds depending on the input parameters. This was a 10x speed up after I used the profiler on my function, NOT on the whole script. Found that I was spending a lot of time passing large structures between functions within the main function. Mostly because I was lazy. Trimmed this up and got much better results.
Add parfor with 12 cores and I was able to get through my DOEs in days rather than weeks.