Root mean square deviations in structure
The
root mean square deviation (
) of certain atoms in a
molecule with respect to a reference structure can be calculated with
the program
gmx rms by least-square fitting the structure to the
reference structure (
) and subsequently calculating the
(
(458)).
where and is the
position of atom at time . Note that fitting
does not have to use the same atoms as the calculation of the
; e.g. a protein is usually fitted on the backbone atoms
(N, C, C), but the can be computed of the
backbone or of the whole protein.
Instead of comparing the structures to the initial structure at time
(so for example a crystal structure), one can also calculate
(458) with a structure at time . This
gives some insight in the mobility as a function of . A
matrix can also be made with the as a function of
and , which gives a nice graphical interpretation
of a trajectory. If there are transitions in a trajectory, they will
clearly show up in such a matrix.
Alternatively the can be computed using a fit-free method
with the program gmx rmsdist:
(459)
where the distance r between atoms at time
is compared with the distance between the same atoms at time
.