In this repository there are: mdp files: for equilibration and production runs. One of the production runs have electric field gro files: CFTR protein states to aid orienting and aligning before applying analysis scripts tcl files: mainly pertains to the analysis of ions inside the pore MOLE2 related files: parameters are in "input.xml"; running MOLE2 using shell script "mole2tunnel.sh"; "mole2.py" has functions that help parse outputs of MOLE2 We are experimenting this format of standardized repositories for research work. For inquiries, contact author Zhi Wei Zeng at wilson.zeng@mail.utoronto.ca

This record contains some files corresponding to some workflows used in our published journal article "Molecular dynamics study of Cl− permeation through cystic fibrosis transmembrane conductance regulator (CFTR)" (DOI: 10.1007/s00018-022-04621-7) Some files that are used to perform analysis that are not part of the standard analysis of MD are provided here. An example is the MOLE2 analysis -- because it is the only program I found that worked on path detection and parametrization in this channel.