This repository contains trajectories, input files, and analysis scripts associated with the manuscript "Constant-pH simulation of the human β2 adrenergic receptor inactivation". The data is organised as follow: - input_files Contains folders for each simulated pH condition (pH_4 to pH_9). Each folder includes: Molecular Dynamics Parameter (MDP) files used for system preparation and production with GROMACS Topology file (topol.top) System coordinate file (conf.gro) Index file (index.ndx) Force field folder (charmm36-mar2019-cphmd.ff) - scripts Example Jupyter notebooks used for analysis: cl_binding_H93.ipynb: Identification of Cl⁻ binding events on His93 lambda.ipynb: Analysis of lambda values microswitches.ipynb: Plotting of microswitch data na_binding.ipynb: Identification of Na⁺ binding events rmsd.ipynb: RMSD data plotting - trajectories Contains folders for each pH condition (pH_4 to pH_9), with subfolders for each of the five replicas (rep1 to rep5). Each replica folder includes: full.pdb: Full system coordinate file full.xtc: Full system trajectory file (1000 ps stride) protein_na.pdb: Coordinate file for protein and Na⁺ ions protein_na.xtc: Trajectory file for protein and Na⁺ ions (100 ps stride) step7.edr: Energy file