Plot Radius of Gyration (Rg)

Overview and Methodology

What It Does

This script calculates the Radius of Gyration (Rg) over time for up to four atom groups in a molecular dynamics simulation. The Rg describes how spatially extended a group of atoms is with respect to its center of mass or geometry, a key indicator of compaction or unfolding.

How It Works

• Objective: Quantify and compare how "spread out" different selections are over the simulation.
• Process:
  • Centering: Calculates the center of mass (or geometry).
  • Rg Calculation: Computes the average distance of atoms from this center — mass-weighted if selected.
  • Multi-Group Support: Allows simultaneous analysis of up to four groups.
  • Visualization: Plots Rg vs. time for all selections, with optional smoothing.

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory.
• Atom groups should be well-defined and stable throughout the simulation.

Key Configuration Options

• Selections:

  • group1_sel–group4_sel: Up to four atomic groups.
  • group1_name–group4_name: Labels for the plotted curves.

• Rg Method:

  • mass_weighted=True: Uses atomic mass for center and distance calculation.
  • mass_weighted=False: Uses geometric (equal-weighted) center and distance.
  • num_bins: Number of bins for Rg histogram.

• Rolling Average:

  • plot_rolling_average=True: Adds smoothed curves using a moving average (rolling_window size).

• Plot Settings:

  • Fully customizable figure size, labels, fonts, and color palettes.

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Output

• Rg Line Plot: figures/*_Rg.png — Shows Rg vs. time for each defined group. Each line reflects structural compactness or unfolding trends.

• Rg Distribution Histogram: figures/*_Rg_histogram.png — Shows Rg distribution over the course of the entire simulation.

• Console Output:

  • Confirmation of defined selections.
  • Frame count and simulation time range.
  • Save path for the final plot image.

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Interpreting the Results

• Stable Rg:

  • Indicates structural integrity or a well-packed region.
  • Common for rigid domains or folded proteins.

• Increasing Rg:

  • Suggests unfolding, expansion, or dissociation.
  • Typical for denaturation or ligand unbinding studies.

• Decreasing Rg:

  • Indicates compaction or aggregation.
  • May reflect folding events or collapsing disordered segments.

• Synchronized Rg Changes:

  • May highlight coordinated transitions between groups, such as domain–domain movements.

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Example Scenarios

Folding Kinetics

• Scenario: Simulate a peptide starting from an extended state.
• Observation: Gradual decrease in Rg.
• Interpretation: Folding or collapse into a compact structure.

Ligand-Induced Expansion

• Scenario: A ligand binds and induces expansion of a flexible domain.
• Observation: Rg of that domain increases sharply after ligand contact.
• Interpretation: Ligand perturbs domain structure or solvation dynamics.

Complex Stability

• Scenario: Compare bound and unbound states of a protein–ligand system.
• Observation: Bound system shows reduced Rg fluctuation.
• Interpretation: Ligand stabilizes local or global structure.

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Usage Tips

• Selection Strategy:

  • Use consistent residue ranges or segments across groups for fair comparison.
  • Include and protein if needed to restrict selection to relevant atoms.

• Mass Weighting:

  • Use mass_weighted=False if you're comparing geometric shape/volume.
  • Use True for physical realism in protein systems.

• Smoothing:

  • Use a rolling_window of 5–10 for long or noisy trajectories to improve trend visibility.

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