Optimal control simulations of musculoskeletal models can be used to reconstruct motions measured with optical motion capture to estimate joint and muscle kinematics and kinetics. These simulations are mutually and dynamically consistent, in contrast to traditional inverse methods. Commonly, optimal control simulations are generated by tracking generalized coordinates in combination with ground reaction forces. The generalized coordinates are estimated from marker positions using, for example, inverse kinematics. Hence, inaccuracies in the estimated coordinates are tracked in the simulation. We developed an approach to reconstruct arbitrary motions, such as change of direction motions, using optimal control simulations of 3D full-body musculoskeletal models by directly tracking marker and ground reaction force data. For evaluation, we recorded three trials each of straight running, curved running, and a v-cut for 10 participants. We reconstructed the recordings with marker tracking simulations, coordinate tracking simulations, and inverse kinematics and dynamics. First, we analyzed the convergence of the simulations and found that the wall time increased three to four times when using marker tracking compared to coordinate tracking. Then, we compared the marker trajectories, ground reaction forces, pelvis translations, joint angles, and joint moments between the three reconstruction methods. Root mean squared deviations between measured and estimated marker positions were smallest for inverse kinematics (e.g., 7.6 ± 5.1 mm for v-cut). However, measurement noise and soft tissue artifacts are likely also tracked in inverse kinematics, meaning that this approach does not reflect a gold standard. Marker tracking simulations resulted in slightly higher root mean squared marker deviations (e.g., 9.5 ± 6.2 mm for v-cut) than inverse kinematics. In contrast, coordinate tracking resulted in deviations that were nearly twice as high (e.g., 16.8 ± 10.5 mm for v-cut). Joint angles from coordinate tracking followed the estimated joint angles from inverse kinematics more closely than marker tracking (e.g., root mean squared deviation of 1.4 ± 1.8 deg vs. 3.5 ± 4.0 deg for v-cut). However, we did not have a gold standard measurement of the joint angles, so it is unknown if this larger deviation means the solution is less accurate. In conclusion, we showed that optimal control simulations of change of direction running motions can be created by tracking marker and ground reaction force data. Marker tracking considerably improved marker accuracy compared to coordinate tracking. Therefore, we recommend reconstructing movements by directly tracking marker data in the optimal control simulation when precise marker tracking is required.