Na+ conductance through the 6NQ0 pore

Result: 5 completed cytosolic-gate-to-selectivity-filter/lumen Na+ permeation events, 0 reverse events counted by the requested positive-branch workflow, and 0 incomplete pore visits. Across 168.0 ns, the signed current is -4.7683828393 pA and the signed conductance is -6.3578437857 pS (magnitude 6.3578437857 pS) at the run-config voltage of -750 mV.

Analysis used MDAnalysis with structure.gro as topology and the supplied trajectory.xtc, selecting Na+ only as resname SOD (180 ions). Protein gate residues 308, 312, 690 and 694 and filter residues 271, 272, 652, 653 and 654 excluded hydrogens. Initial geometry was evaluated at XTC frame 0; the GRO supplied topology rather than a separate coordinate frame. The trajectory contains 1,681 frames, from 0.0 to 168.0 ns.

Notebook-style pore candidates were built by scanning every other trajectory frame and retaining unique Na+ atom indices within 6.0 Angstrom in xy of the initial gate centre of mass, without a z restriction. This yielded 167 candidate ions. Initial fixed boundaries were cytosolborder=63.2 Angstrom and lumenborder=84.3 Angstrom; exit_threshold=max(initial filter z)+2.0=91.5 Angstrom.

The persistent event state machine was applied to candidates at every frame. Entry was first marked at abs(z-cytosolborder)<=2.0 Angstrom. After entry, an ion reached the inside state when its z lay between the gate and filter borders and its xy distance to either the frame's gate or filter centre of mass was <=6.0 Angstrom. Once inside, reaching z>=91.5 Angstrom completed an event. Continuous residence in a gate-centred cylinder was not required, and leaving that cylinder did not reset entry or inside status. Completion reset the ion's state for a potential subsequent event. An inside-state ion without a completed exit at trajectory end would be incomplete; entry-only ions were excluded. The positive branch does not independently search for reverse transfers.

Completed events (0-based atom indices and frame indices; trajectory times in ns):
atom 23308: entry 7.3 ns (frame 73), exit 11.6 ns (frame 116).
atom 23333: entry 10.8 ns (frame 108), exit 50.1 ns (frame 501).
atom 23262: entry 45.5 ns (frame 455), exit 59.7 ns (frame 597).
atom 23307: entry 70.6 ns (frame 706), exit 94.7 ns (frame 947).
atom 23370: entry 159.3 ns (frame 1593), exit 167.8 ns (frame 1678).
All five have direction cytosolic_gate_to_selectivity_filter_lumen and completed_full_permeation=true.

Using elementary charge e=1.602176634e-19 C and the requested gate-to-filter negative reporting convention:
net ion count = 5 - 0 = 5;
net_charge_C = -5e = -8.01088317e-19 C;
I = net_charge_C/(168.0e-9 s) = -4.768382839285714e-12 A;
G = I/abs(-0.750 V) = -6.357843785714285e-12 S = -6.3578437857142855 pS.
The negative conductance is the specified signed reporting convention; its magnitude is positive.

Two independently implemented analyses of the original trajectory agreed on candidate identities, geometry, completed events, timing, incomplete visits, and calculated current/conductance. Using moving versus fixed gate/filter xy centres or sequential versus exclusive state transitions did not change these event records. The CSV schemas and arithmetic were separately validated.

The observed completed Na+ permeation events support measurable conductance through the 6NQ0 pore during this trajectory under the notebook definition. This finite-trajectory estimate is based on five events at one applied voltage and does not establish a full current-voltage relation.

Required output files:
/workspace/workspaces/1788723639974521/benchmark/31_traj_ana_na_conductance_6nq0/outputs/na_transfer_events.csv
/workspace/workspaces/1788723639974521/benchmark/31_traj_ana_na_conductance_6nq0/outputs/conductance_summary.csv
/workspace/workspaces/1788723639974521/benchmark/31_traj_ana_na_conductance_6nq0/final_answer.txt