Input and analysis scripts for the paper "Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning"
Software packages used: NAMD2, VMD (https://www.ks.uiuc.edu/Development), ColVars (https://github.com/Colvars/colvars/tree/master/namd), PLUMED (https://www.plumed.org), PyCaret (https://pycaret.org)
Metadynamics: ligand dissociation and residence time approximation
-- Simulation inputs (NAMD2)
-- Postprocessing analysis with PLUMED
-- Residence time calculations
ML_regression_analysis: characterize important ligand-residue interaction pairs governing residence times
-- Data files (zipped)
-- Analysis workflow in Jupyter notebook