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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.
Next: Parameters
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pellegrini eric
2009-10-06