.. MasterMSM documentation master file, created by sphinx-quickstart on Mon Mar 25 23:47:22 2019. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ========================================== Welcome to MasterMSM's documentation! ========================================== MasterMSM is a Python package for generating Markov state models (MSMs) from molecular dynamics trajectories. We use a formulation based on the chemical master equation. This package will allow you to: * Create Markov state / master equation models from biomolecular simulations. * Discretize trajectory data using dihedral angle based methods useful for small peptides. * Calculate rate matrices using a variety of methods. * Obtain committors and reactive fluxes. * Carry out sensitivity analysis of networks. We have written a `paper `_ on MasterMSM that briefly describes some of the code capabilities. The MasterMSM code is hosted in `Github `_. Active development of the MasterMSM code takes place using the git version control system. .. toctree:: :maxdepth: 3 :caption: Contents: about installation documentation support Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`