Living Journal of Computational Molecular Science · 2018 · 67 citations · 0 references
EngineeringMolecular BiologyMarkov State ModelingComputational ChemistryMarkov Chain Monte CarloMolecular DynamicsMolecular GraphicState EstimationMarkov ChainsHidden Markov ModelSystems EngineeringKinetics (Physics)Modeling And SimulationMolecular KineticsBiophysicsProbability TheoryComputer ScienceMarkov Decision ProcessTutorial NotebooksNatural SciencesMarkov KernelProcess ControlPyemma SoftwareSystems BiologyChemical KineticsComputational Biophysics
This tutorial provides an introduction to the construction of Markov models of molecular kinetics from molecular dynamics trajectory data with the PyEMMA software. Using tutorial notebooks, we will guide the user through the basic functionality as well as the more common advanced mechanisms. Short exercises to self check the learning progress and a notebook on troubleshooting complete this basic introduction.