About

In the last decade, Master equation / Markov state models (usually termed MSMs) have become one of the key methodologies to analyze data from molecular dynamics (MD) simulations. You can find information about MSMs in general in the following volume

• An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, edited by Pande, Bowman and Noe (Springer, 2014).

The MasterMSM library brings a different flavour of MSMs, based on the methods introduced by N. V. Buchete and G. Hummer (J. Phys. Chem. B, 2008). The central difference relies in that instead of using transition matrices we focus in rate matrices, which determine the time evolution of the system as described by the chemical master equation.