Plot RMSF (Root Mean Square Fluctuation)

Overview and Methodology

What It Does

This script calculates the Root Mean Square Fluctuation (RMSF) of atoms over a simulation trajectory to quantify the positional flexibility of regions or residues. It supports up to four groups and can report either:

• One RMSF value per group
• One RMSF value per residue (if plot_individual = True)

How It Works

• Trajectory Alignment: Each group is aligned to itself in the first frame to remove global motion.
• RMSF Calculation:
  • Measures the average deviation of atomic positions from their mean over time.
  • Uses either all atoms in the selection or per-residue averages.
• Visualization: Plots RMSF as a bar chart, colored by group.

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Configuration and Inputs

Selections

• groupX_sel (1–4): Atom selections (e.g., "segid VSD and protein")
• groupX_name: Labels for legend/group coloring
• plot_groupX_individual: Whether to compute RMSF per residue (True) or as a group average (False)

Frame Settings

• begin_frame, end_frame, step: Frame range and sampling
• time_total: Used only for labeling

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Output

• RMSF Bar Plot
  figures/<group1_name>_<group2_name>_RMSF.png
  Displays RMSF values for each group or residue with color-coded bars.

• Legend
  If per-residue RMSF is enabled, groups are color-coded and included in the legend.

• Console Output

  • Lists selection details
  • Displays total frames processed
  • Confirms save location

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Interpreting the Results

• High RMSF:
  • Indicates high flexibility or mobility (e.g., termini, loops)
• Low RMSF:
  • Suggests stable, rigid regions (e.g., helices, core residues)
• Comparative Insight:
  • Helps identify differential dynamics across groups or domains
  • Useful for analyzing the effect of mutations, ligand binding, or conformational changes

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Example Scenarios

Membrane Channel Domain Comparison

• group1_sel = "segid VSD", group2_sel = "segid POI"
• Observation: VSD shows lower RMSF
• Interpretation: VSD is more rigid than interacting domain

Per-Residue Flexibility of a Peptide

• group1_sel = "segid TOX and resid 1 to 20"
• plot_group1_individual = True
• Observation: Residues 1–5 show the highest RMSF
• Interpretation: N-terminus is more flexible than rest of the peptide

Mutant vs. Wild-Type RMSF

• Use different selections for WT and mutant simulations
• Insight: Can reveal stabilization/destabilization at specific sites

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Usage Tips

• Exclude Water: Automatically excludes TIP/WAT residues from calculation
• Alignment is per group: Each selection is internally aligned to itself, not globally
• Per-residue RMSF is slower: Uses more memory and CPU time, but more informative

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