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

Simulating cw-ESR Spectrum Using Discrete Markov Model of Single Brownian Trajectory