Analysis of the molecular dynamics trajectories
There are many types of analysis that can be performed given a molecular dynamics trajectory. The example program here calculates the radii of gyration of the trajectory structures and the RMS coordinate deviations between these structures and the starting structures. However, the program should serve as a template for the calculation of other types of quantity, such as those which indicate how close a structure is to the stable folded form of the protein.
This example is based upon Example 17 of the pDynamo distribution.