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Theory and implementation

ROG is the name of several related measures of the size of an object, a surface, or an ensemble of points. It is calculated as the Root Mean Square Distance between the system and a reference that can be either the center of gravity of the system either a given axis. In nMOLDYN, the reference is choosen to be the center of gravity of the system under study. Mathematically, it can be defined as:

| (4.32)

where is the number of atoms of the system, and and are respectively the position of atom and the center of mass of the system at time .

ROG describes the overall spread of the molecule and as such is a good measure for the molecule compactness. For example, it can be useful when monitoring folding process.

In nMOLDYN, ROG is computed using the discretized version of equation 4.32:

| (4.33)

where is the number of frames and is the time step.

Next: Parameters Up: Radius of gyration Previous: Radius of gyration Contents