Plotting Instantaneous Values Along the Trajectory

Molecular dynamics is essentially a study of the evolution in time of energetic and structural molecular data. The data is often best represented as a graph of a molecular quantity as a function of time. The values to be plotted can be any quantity x that is being averaged over the trajectory, or the standard deviation, Dx. You can create as many as four simultaneous graphs at once. 

While you can follow the progress of a trajectory, you cannot get publication quality graphs from HyperChem. You can, however, use the information in the CSV file with other programs for creating graphs for publication. 

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