Introductory Jupyter Modules

A place to put some introductory resources on various sampling/analysis techniques. 

These were originally developed for Advanced Special Topics in Chemical Theory, taught by Prof. Aaron Dinner in the Spring of 2019. The Ising Model/Umbrella Sampling module was adapted from an example generously provided by Prof. Glen Hocky at NYU, a former postdoc in the group. 

2D Ising Model / Intro to Umbrella Sampling

2DIsing_Module.ipynb

2DIsing_Key.ipynb

Intro to PyEMMA / Markov State Modeling

MSM_Key.ipynb

MSM_Module.ipynb

The data for MSM notebooks, as well as duplicates of these Jupyter notebooks, are available on Midway3 (/project/dinner/intro_modules/)