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Theory and implementation

The RMSD is maybe the most popular estimator of structural similarity. It is a numerical measure of the difference between two structures that can be defined as:

| (4.30)

where is the number of atoms of the system, and and are respectively the position of atom at time and where is a reference time usually choosen as the first step of the simulation. Typically, RMSD is used to quantify the structural evolution of the system during the simulation. It can provide precious information about the system especially if it reached equilibrium or conversely if major structural changes occured during the simulation.

In nMOLDYN, RMSD is computed using the discretized version of equation 4.30:

| (4.31)

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

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