Anyone interested in learning how to use Markov state models to analyse molecular simulations.
- Basic Python knowledge
- Basic Linear algebra
- Basic knowledge of setting up and running molecular simulations
Markov State Models (MSM) are a set of tools to analyse molecular simulation trajectories in order to obtain estimates of long-timescale dynamics and free energies for the system of study. MSMs have been used in the past to study short term dynamics such as side chain rearrangements, to much longer dynamical properties such as protein folding, allostery, or protein-protein association. This workshop will give an introduction to the theory behind MSMs followed by a hands-on session on building an MSM. Essential steps such as clustering the simulation data, estimation of the MSM and validation of the MSM as well as the MSMs physical interpretations will be covered. We will be using pyEMMA as the software framework throughout the workshop.
The training material consists of several notebooks:
01_IO_Clustering.ipynb
02_estimation_validation.ipynb
03_msm_analysis.ipynb
04_pcca_tpt.ipynb
For Installation instructions please see the pyemma website: pyemma.org
If you want to get started with some more background reading for MSMs these are references are a good starting point:
[1]Prinz, Jan-Hendrik and Wu, Hao and Sarich, Marco and Keller, Bettina and Senne, Martin and Held, Martin and Chodera, John D. and Schütte, Christof and Noé, Frank. 2011. Markov models of molecular kinetics: Generation and validation. URL
[2]Gregory R. Bowman and Vijay S. Pande and Frank Noé. 2014. An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. URL
[3]Brooke E. Husic and Vijay S. Pande. 2018. Markov State Models: From an Art to a Science.
And of course the pyemma tutorial manuscript this material is based on:
[4]Wehmeyer et al 2018. Introduction to Markov state modeling with the PyEMMA software. URL
Antonia Mey @ppxasjsm (github.com/ppxasjsm)
Please raise issues on github with bugs or comments.
