Plot Ion Conduction Through a Channel

Overview and Methodology

What It Does

This script tracks the movement of ions through a channel’s selectivity filter (SF) across a molecular dynamics trajectory. It identifies ions near the SF, corrects for periodic boundary conditions (PBCs), detects complete ion crossings, and visualizes ion z-axis positions over time. If an electric field is provided, it estimates single-channel conductance based on observed ion permeation events.

How It Works

• Objective: Quantify ion passage through the channel and correlate this with applied potential.
• Process:
  • Aligns trajectory to the SF reference to stabilize orientation.
  • Tracks z-position and xy-distance of ions relative to the SF center.
  • Applies PBC correction for continuity in ion traces.
  • Detects crossings based on:
    • Direction of movement
    • Entry/exit criteria
    • Minimum traversal through the SF region
  • Computes single-channel conductance using:

$G = \frac{N \cdot e}{V \cdot t}$

Where:

• $N$ = number of ion crossings
• $e = 1.602 \times 10^{-19}$ C (elementary charge)
• $V$ = applied voltage (in Volts)
• $t$ = simulation duration (in seconds)

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory aligned to the channel axis (z-axis).

Key Configuration Options

• Selectivity Filter and Ions:

  • sf_sel: Atom selection for the selectivity filter (SF).
  • ion_sel: Selection of the ion species to track (e.g., resname POT).

• Trajectory Alignment:

  • Aligns entire trajectory to the SF selection for consistent tracking.

• Tracking Parameters:

  • xy_radius: Maximum xy distance from z-axis to consider an ion “in” the SF. Can be set manually or auto-detected.
  • z_buffer: Defines vertical bounds above and below the SF for tracking and plotting.

• Directionality:

  • ion_direction: 'up' or 'down' — expected conduction direction based on field polarity.

• Conductance Parameters:

  • electric_field_mv: Voltage across the channel (mV).
  • time_unit: Simulation duration unit (ps, ns, µs) for conductance calculation.

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Output

• Plot:

  • File: ion_conduction.png
  • Y-axis: z-position of each ion over time.
  • Horizontal dashed lines mark the SF boundaries.
  • Breaks and re-entry are adjusted for PBC and plotted continuously with gap indicators.

• Console Output:

  • Number of total ion crossings.
  • Estimated conductance (in picosiemens, pS).
  • Debug info for PBC transitions (optional).

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Interpreting the Results

• Crossing Events:

  • Detected based on:
    • Start inside the SF and exit in correct direction.
    • Entry from one side, traversal through ≥30% of SF z-range, and exit in expected direction.

• Z-traces:

  • Smooth trajectories through SF imply conduction events.
  • Gaps indicate PBC jumps or movement outside tracking bounds.

• Conductance Estimate:

$G = \frac{N \cdot e}{V \cdot t}$

• For:
  • $N = 12$ ions
  • $V = 100$ mV = $0.1$ V
  • $t = 300$ ns = $3 \times 10^{-7}$ s

$\Rightarrow G = \frac{12 \cdot 1.602 \times 10^{-19}}{0.1 \cdot 3 \times 10^{-7}} \approx 64.1$ pS

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Example Scenarios

High-Conductance Channel

• Observation: Multiple ions cross SF during the trajectory.
• Result: High estimated conductance (e.g., >100 pS).
• Interpretation: Strong permeation consistent with open state.

Blocked or Inactive Channel

• Observation: Ions enter but do not traverse SF.
• Result: No crossings, conductance = 0.
• Interpretation: Suggests a closed, collapsed, or occluded pore.

Directional Conduction

• Observation: Crossings only in up direction under positive potential.
• Interpretation: Rectification or voltage-gated preference.

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Usage Tips

• Ion Selection:

  • Match ion name with topology file (e.g., resname POT, CLA, SOD).
  • Use ion_direction to align with expected electrochemical gradient.

• PBC Artifacts:

  • Use debug_pbc=True to troubleshoot jumps or unexpected exits.

• Plot Readability:

  • Adjust z_buffer for tall channels.
  • Adjust xy_radius for narrow vs. wide pores.

• Conductance Validation:

  • Resulting pS values should be compared to known experimental data.

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