  We use recently developed primitive path analysis (PPA) methods to study the
effect of equilibration on entanglement density in model polymeric systems.
Values of N_e for two commonly used equilibration methods differ by a factor of
two or three even though the methods produce similar large-scale chain
statistics. We find that local chain stretching in poorly equilibrated samples
increases entanglement density. The evolution of N_e with time shows that many
entanglements are lost through fast processes such as chain retraction as the
local stretching relaxes. Quenching a melt state into a glass has little effect
on N_e. Equilibration-dependent differences in short-scale structure affect the
craze extension ratio much less than expected from the differences in PPA
values of N_e.
