Plot RMSD (Root Mean Square Deviation)

Overview and Methodology

What It Does

This script calculates the Root Mean Square Deviation (RMSD) over time for up to four atomic groups within a molecular dynamics simulation. RMSD provides insight into how much a structure deviates from its initial conformation, serving as a key metric for assessing structural stability and conformational changes.

How It Works

• Objective: Quantify structural deviations during a trajectory for selected atom groups.
• Process:
  • Alignment: Each frame is aligned to a reference frame (typically the first) using a specified atom selection.
  • RMSD Calculation: Measures the average positional deviation of atoms from their reference positions.
  • Per-Residue Option: Allows for RMSD calculation at the residue level for fine-grained analysis.
  • Multi-Group Support: Supports up to four simultaneous group selections.
  • Rolling Average: Optionally overlays a smoothed curve using a rolling window.

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Configuration and Inputs

Prerequisites

• Requires a loaded trajectory.

Key Configuration Options

• Selections:

  • group1_sel–group4_sel: Define up to four atomic groups using MDAnalysis selection strings.
  • group1_name–group4_name: Custom labels for each group.

• Per-Residue Analysis:

  • plot_groupX_individual=True: Enables per-residue RMSD for group X.

• RMSD Method:

  • 'All Atoms': Uses all atoms in the selection.
  • 'Backbone': Restricts to backbone atoms (N, CA, C).
  • 'CA': Uses only alpha-carbon atoms.

• Frame Range:

  • begin_frame, end_frame, step: Defines trajectory slicing (e.g., skip frames, partial sampling).

• Simulation Duration:

  • time_total: Total duration of the trajectory (used for X-axis).

• Rolling Average:

  • plot_rolling_average=True: Adds smoothed curve.
  • rolling_window: Number of frames in the rolling window.

• Plot Customization:

  • fig_width, fig_height: Plot dimensions.
  • title_label, xlabel, ylabel: Axis titles and their font sizes.
  • sns_style, color_palette: Aesthetic settings for consistent styling.
  • legend_size: Font size for legend.

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Output

• RMSD Plot: figures/*_RMSD.png — RMSD vs. time plot for each group or per-residue RMSD curves if selected.

• Console Output:

  • Defined group selections and options.
  • Confirmation of processed frame range.
  • Path to saved plot.

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Interpreting the Results

• Stable RMSD:

  • Indicates minimal deviation from the reference frame.
  • Common for well-folded domains or highly rigid regions.

• Gradual Increase:

  • Suggests conformational change, flexibility, or drift.
  • Often observed in loop regions or solvent-exposed segments.

• High RMSD with Fluctuations:

  • Reflects dynamic, unstable regions or unfolding events.

• Per-Residue Trends:

  • Peaks may highlight flexible loops or mobile sidechains.
  • Flat traces often correlate with structured, stable residues.

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Example Scenarios

Protein Stability

• Scenario: Simulate a folded protein over 500 ns.
• Observation: Flat RMSD around 1–2 Å.
• Interpretation: Structure is stable over the simulation.

Domain Movement

• Scenario: Large protein with mobile subdomains.
• Observation: RMSD gradually increases to 5 Å.
• Interpretation: Subdomain movement or hinge flexibility.

Residue-Specific Flexibility

• Scenario: Use per-residue RMSD for a loop region.
• Observation: Certain residues show larger deviations.
• Interpretation: Indicates local flexibility or disorder.

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Usage Tips

• Selection Strategy:

  • Use and not resname TIP WAT to exclude solvent.
  • Choose selections that make structural sense (e.g., specific chains or domains).

• CA vs Backbone vs All Atoms:

  • Use 'CA' for global motions and quick comparisons.
  • Use 'Backbone' or 'All Atoms' for higher accuracy or fine motions.

• Smoothing:

  • Use rolling_window=3–5 for typical smoothing. Adjust based on trajectory length.

• Per-Residue View:

  • Recommended for detailed insights but may generate clutter; use filtering or post-processing for clarity.

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