The Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is an enhanced conformational sampling to promote structural transitions from a given reactant. We here assessed how a number of initial structures, ninitial, affected the conformational sampling efficiency. We provide clear evidence that a large ninitial accelerated structural transitions. In contrast, a small ninitial showed a high conformational sampling efficiency as an accumulated simulation time over cycles, indicating that both ninitial values are suitable for promoting structural transitions.