MD simulations for the article: An atomic interaction conserved for over 4 billion years gates inhibitory neurotransmission

File naming Files are named system__replicate__file (fields separated by underscores), reflecting the original folder structure. For example, Leu140_Closed__rep1__md.xtc is the trajectory for the WT Leu140 channel in the Closed state, replicate 1. system prefix — Leu140 (or leu140) denotes wild-type leucine at position 140; Lah140 denotes the non-canonical amino acid Lah at position 140. state — the channel state the simulation started from: Desensitized (derived from PDB 6X3Z), Closed (from PDB 6X3S), or Open (from an advanced-sampling system design, https://zenodo.org/records/10964268). replicate — rep1–rep4. Each of the four conditions (lah140_Desensitized, leu140_Desensitized, leu140_Open, leu140_Closed) was run four times. file type — md.pdb is the starting structure; md.xtc is the trajectory. Topology and Restraint Files If the file ends in "_toppar" these are the topology files and if the files end in "_restraints" these are the restraints. Each were used during minimization, equilibration, and production. For more details, see the referenced publication