A constant-energy molecular dynamics simulation is used to monitor protein motion at zero-total angular momentum. With a simple protein model, it is shown that overall rotation is possible at zero-total angular momentum as a result of flexibility. Since the rotational motion is negligible on a time scale of 1000 reduced time units, the essentially rotation-free portion of the trajectory provides an unbiased test of the common approximate methods for separating overall rotation from internal motions by optimal superposition. Removing rotation by minimizing the root-mean-square deviation (RMSD) for the entire system is found to be more appropriate than using the RMSD for only the more rigid part of the system. The results verify the existence of positive cross-correlation in the motions of atoms separated by large distances.
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