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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
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pellegrini eric
2009-10-06