Molecular Dynamics simulations suggest possible activation and deactivation pathways in hERG channel

equil_gating_4_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 4 equilibration trajectory equil_gating_6_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 6 equilibration trajectory equil_gating_8_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 8 equilibration trajectory equil_gating_4.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 4 equil_gating_6.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 6 equil_gating_8.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 8 equil_open_assembly_xleap.prmtop: file topology of the hERG open state equilibration trajectory equil_open.dcd: 100 ns NPT trajectory of the hERG open state herg_closed_gating_4.pdb: PDB file of hERG closed state with gating charge 4 after Steered MD simulations herg_closed_gating_6.pdb: PDB file of hERG closed state with gating charge 6 after Steered MD simulations herg_closed_gating_8.pdb: PDB file of hERG closed state with gating charge 8 after Steered MD simulations TMD_O-C_closed_gating_8_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 8 TMD trajectory TMD_O-C_closed_gating_6_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 6 TMD trajectory TMD_O-C_closed_gating_4_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 4 TMD trajectory TMD_O-C_closed_gating_8.dcd: TMD trajectory of the hERG closed state with gating charge 8 TMD_O-C_closed_gating_6.dcd: TMD trajectory of the hERG closed state with gating charge 6 TMD_O-C_closed_gating_4.dcd: TMD trajectory of the hERG closed state with gating charge 4 MD trajectories (equilibration and Targeted MD trajectories) in dcd format can be visualized using visualization tools such as VMD or PyMol after uploading the topology file. The directory data_supplementary-note-4.tar.bz2 contains the files related to the Supplementary Notes 4: "A practical example of pathway calculation".