Clock synchronization is an essential problem faced by packet transport network. PTP (precise time protocol) can be used to solve this problem. Its feasibility has been verified by related literatures. In this paper, we use the OPNET simulation platform to further study the key factors affect the clocks' accuracy of packet-based synchronization schemes, e.g., queuing disciplines, number of nodes that PTP messages have passed, deployment of the PTP enabled router, and network traffic load. We intend to answer the question how much influence can each factor make to the clocks' synchronization performance.