  Dynamic trajectories can be modeled with a Markov State Model (MSM). The
reduction of continuous space coordinates to discretized coordinates can be
done by statistical binning process. In addition to that, the transition
probabilities can be determined by recording each event in the dynamic
trajectory. This framework is put to a test by the electron spin resonance
(ESR) spectroscopy of nitroxide spin label in X- and Q- bands. Calculated
derivative spectra from MSM model with transition matrix obtained from a single
Brownian trajectory by statistical binning process with the derivative spectra
generated from the average of a large number of Brownian trajectories, are
compared and yield a very good agreement. It is suggested that this method can
be implemented to calculate absorption spectra from molecular dynamics (MD)
simulation data. One of its advantages is that due to its reduction of
computational effort, the parametrization process will be quicker. Secondly,
the transition matrix defined in this manner, may indicate separable potential
changes during the motion of the molecule and may have advantages when working
with reducible set of coordinates. Thirdly, one can calculate the ESR spectra
from a single MD trajectory directly without extending it artificially in the
time axis. However, for short MD trajectories, the required statistical
information can not be obtained depending on the timescale of transitions.
Therefore, some statistical improvement will be needed in order to reach a
better convergence.
