Supporting data for: "Constant-pH simulation of the human β2 adrenergic receptor inactivation"

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