MSM sensitivity (msmsense)

This is a package for bootstrapping Markov state model observables from molecular dynamics simulations. It should be used alongside MSM sensitivity analysis (sensetools) to recreate the data for the paper Sensitivity and optimisation of Markov state models for biomolecular systems.

Installation

1. Create a conda/mamba environment and cd to root of this repo.
2. mamba install numpy pandas pyyaml mdtraj pyemma scipy click -y
3. pip install hyperopt
4. pip install -e .

Use

See the README of sensetools for practical use.

To see the available commands simply use the help function on the cli:

$ msmsense --help

To change the limits of the hyperparameter search space edit the msmsense/searchspace.yaml file.