Simulation inputs, analysis notebooks and representative structures for the paper "TRPP Ion Channels Function in the π-Conformation Rather Than the α-Conformation" by Chenfeng Zhang, Wojciech Kopec and Julien Michel.
Systems follow Supplementary Table S1 and simulation sets follow Supplementary Table S2.
Trajectories supporting the main conclusions, with a reduced number of frames, are available on Zenodo (https://doi.org/10.5281/zenodo.23946105).
01_systems/ simulation boxes, split by force field
CHARMM/ CHARMM36m + CHARMM-modified TIP3P
OPC/ AMBER ff19SB + OPC + 12-6-4 ions
NN_<system>/ step5_input.gro, index.ndx, topol*.top and toppar*/
02_simulations/ GROMACS .mdp and PLUMED input files, split by force field
CHARMM/
OPC/
03_scripts/ analysis notebooks
pore_hydration.ipynb water density along the pore axis
permeation.ipynb ion permeation events and conductance
trp_survey.ipynb lower-gate survey of TRP channel cryo-EM structures
04_snapshots/ representative structures shown in the figures