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Abstract
We have carried out a very long (300 ps) molecular dynamics simulation of the protein
myoglobin. This trajectory is approximately three times longer than the longest previous
molecular dynamics simulation of a protein, and ten times longer than protein simulations
of comparable size (1,423 atoms in our model). Here we report results from this long
simulation concerning the average structure, the mean square fluctuations of atoms
about the average structure, and the nuclear magnetic resonance order parameters for
various groups in myoglobin. The results demonstrate that the average coordinates
change very slowly during the simulation. The relative atomic mobilities are well
described by the simulation. For both the mean square atomic fluctuations and the
order parameters, however, there are significant quantitative differences when values
calculated using shorter portions of the trajectory are compared with results obtained
for the entire 300-ps simulation. The implications of this result for obtaining converged
properties from protein molecular dynamics simulations for comparison with experiment
are discussed.