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Simulation time can start any time. The use_sim_time parameter tells the ROS nodes to expect time to come from the /clock topic rather than the system as explained in the Clock wiki. If you're running a simulation, the simulator may start the clock at 0, but it could just as easily start at some other time. With rosbag, the --clock option publishes the time from the messages in the bag file. You can either manipulate those timestamps in the bag file (offline; the rosbag API may help), or you can deal with it in a node (online). Either way, you'll have to save the stamp from the first message and subtract it from later messages, like you said.