Analysis Features¶

Detailed documentation of GateWizard's trajectory and energy analysis capabilities.

Overview¶

GateWizard provides two main types of analysis:

1. Structural Analysis: For trajectory files (.dcd, .xtc, .trr)
2. Energetic Analysis: For NAMD log files

Both types support multiple files, custom time assignment, and flexible unit selection.

Structural Analysis¶

Supported Formats¶

• Topology: PSF, PDB, GRO
• Trajectories: DCD, XTC, TRR, NetCDF

Analysis Types¶

RMSD (Root Mean Square Deviation)¶

Purpose: Measure structural deviation from a reference structure.

Usage:

1. Select RMSD from Analysis Type
2. Set reference frame (default: first frame)
3. Choose atom selection (e.g., "protein and name CA")
4. Enable/disable alignment
5. Run analysis

Output: - Plot: Time vs RMSD - Data: Time points and RMSD values - Units: Ångstroms (Å) or nanometers (nm)

Interpretation: - Low RMSD (~1-3 Å): Structure remains close to reference - High RMSD (>5 Å): Significant structural changes - Plateau: System has equilibrated - Increasing trend: System still evolving

RMSF (Root Mean Square Fluctuation)¶

Purpose: Identify flexible and rigid regions of the protein.

Usage:

1. Select RMSF from Analysis Type
2. Choose atom selection (typically C-alpha atoms)
3. Run analysis

Output: - Plot: Residue number vs RMSF - Data: Per-residue fluctuation values - Units: Ångstroms (Å) or nanometers (nm)

Interpretation: - Low RMSF (<1 Å): Rigid regions (core, secondary structures) - High RMSF (>2 Å): Flexible regions (loops, termini) - Peaks indicate highly mobile residues

Distance Analysis¶

Purpose: Track distances between specific atoms or groups.

Usage:

1. Select Distances from Analysis Type
2. Define atom pairs:
   - Selection 1: "resid 10 and name CA"
   - Selection 2: "resid 50 and name CA"
3. Run analysis

Output: - Plot: Time vs Distance - Data: Time points and distance values - Units: Ångstroms (Å) or nanometers (nm)

Use Cases: - Salt bridge formation - Domain movements - Ligand-protein interactions - Conformational changes

Radius of Gyration¶

Purpose: Measure overall compactness of the structure.

Usage:

1. Select Radius of Gyration
2. Choose atom selection (typically all protein atoms)
3. Run analysis

Output: - Plot: Time vs Rg - Data: Time points and Rg values - Units: Ångstroms (Å) or nanometers (nm)

Interpretation: - Constant Rg: Stable, compact structure - Increasing Rg: Unfolding or expansion - Decreasing Rg: Compaction or folding

Time Management for Trajectories¶

Without Time Assignment¶

Uses frame numbers × time step: - Automatically calculated from trajectory metadata - Suitable for single, continuous trajectories

With Time Assignment¶

Distributes frames evenly across assigned time:

Example:

File1.dcd: 1000 frames, assigned 10 ns
  → Frame 0: 0.0 ns
  → Frame 500: 5.0 ns
  → Frame 999: 10.0 ns

File2.dcd: 2000 frames, assigned 50 ns
  → Frame 0: 10.0 ns (continues from File1)
  → Frame 1000: 35.0 ns
  → Frame 1999: 60.0 ns

Benefits: - Accurate time representation for concatenated runs - Proper handling of different sampling rates - Sequential placement of multiple simulations

Atom Selections¶

GateWizard uses MDAnalysis selection syntax:

Common Selections:

protein                      # All protein atoms
protein and name CA          # C-alpha atoms only
protein and backbone         # Backbone atoms (N, CA, C, O)
resid 1:50                   # Residues 1 to 50
resname ALA                  # All alanine residues
name CA and resid 10:20      # C-alpha of residues 10-20
segid PROA                   # Atoms in segment PROA

Advanced Selections:

protein and not name H*              # Protein without hydrogens
(resid 10:20) or (resid 50:60)      # Multiple regions
around 5 resname LIG                 # Within 5Å of ligand

Units and Conversions¶

Distance Units: - Ångstroms (Å): Default in structural biology - Nanometers (nm): Common in MD simulations - Conversion: 1 nm = 10 Å

Time Units: - Picoseconds (ps): Fine-grained time scale - Nanoseconds (ns): Common for simulation lengths - Microseconds (µs): Long simulations - Conversions: 1 ns = 1000 ps, 1 µs = 1000 ns

Energetic Analysis¶

NAMD Log File Analysis¶

Supported Data: - ETITLE: Column headers from log file - ENERGY: Data lines with timesteps and values

Available Properties: - TEMP: Temperature (K) - TOTAL: Total energy (kcal/mol) - KINETIC: Kinetic energy (kcal/mol) - POTENTIAL: Potential energy (kcal/mol) - ELECT: Electrostatic energy (kcal/mol) - VDW: van der Waals energy (kcal/mol) - PRESSURE: Pressure (bar) - VOLUME: Volume (Ų)

Time Distribution for Log Files¶

Without Time Assignment¶

Uses timestep (TS) column:

TS = 0:     0 ps
TS = 1000:  2 ps (if timestep=2fs, output every 1000 steps)
TS = 50000: 100 ps

With Time Assignment¶

Distributes data points evenly:

Example:

equilibration.log: 500 points, assigned 5 ns
  → Point 0: 0.0 ns
  → Point 250: 2.5 ns
  → Point 499: 5.0 ns

production.log: 5000 points, assigned 100 ns
  → Point 0: 5.0 ns (continues from equilibration)
  → Point 2500: 55.0 ns
  → Point 4999: 105.0 ns

Benefits: - Correct timeline for multi-stage simulations - Proper spacing for different output frequencies - Sequential representation of simulation phases

Energy Units¶

kcal/mol (default in NAMD): - Standard in US molecular modeling - 1 kcal/mol = 4.184 kJ/mol

kJ/mol (SI unit): - Standard in international publications - Conversion applied automatically when selected

Use Cases: - Plot TOTAL energy to check stability - Monitor TEMP for thermostat performance - Check PRESSURE for barostat performance - Compare KINETIC and POTENTIAL for energy distribution

Multiple Property Plotting¶

Plot multiple properties simultaneously:

1. Select multiple columns (Ctrl+Click)
2. Each property shown in different color
3. Legend automatically added
4. Y-axis label adjusted for multiple properties

Example:

Plot: TOTAL, TEMP, PRESSURE
Result: Three lines showing:
  - Energy evolution (left Y-axis)
  - Temperature stability
  - Pressure fluctuations

Plot Customization¶

Available Options¶

Title and Labels: - Plot Title: Custom description - X-Axis Label: Time (with units) - Y-Axis Label: Property (with units)

Units: - X-Axis: ps, ns, µs - Y-Axis (Distance): Å, nm - Y-Axis (Energy): kcal/mol, kJ/mol

Appearance: - Background Color: Dark Gray, Light Gray, White, Black - Line Color: Blue, Red, Green, etc. - Grid: Automatic with transparency

Ranges: - X-Min, X-Max: Limit time range - Y-Min, Y-Max: Limit value range - Auto-scaling: Enabled by default

Export Options¶

Plot Export: - PNG: Raster image (good for presentations) - SVG: Vector image (good for publications) - High resolution available

Data Export: - CSV: Spreadsheet format

Time(ns),RMSD(Å)
0.0,0.0
0.1,0.5
0.2,0.8

• JSON: Structured format

  {
    "time": [0.0, 0.1, 0.2],
    "rmsd": [0.0, 0.5, 0.8],
    "units": {"time": "ns", "rmsd": "Å"}
  }
  

• NumPy: Python analysis

  import numpy as np
  data = np.load('results.npz')
  time = data['time']
  rmsd = data['rmsd']
  

Advanced Features¶

Draggable File List¶

Reorder files by dragging: 1. Click and hold on file bar handle (☰) 2. Drag to new position 3. Release to reorder 4. Time distribution updates automatically

Real-Time Progress¶

During analysis: - Progress bar shows completion - Status messages update - Can cancel long-running analyses

Batch Processing¶

Analyze multiple trajectories: 1. Add all files at once 2. Assign times for each 3. Run analysis once 4. Data combined automatically

Troubleshooting Analysis¶

Issue: RMSD values too high¶

Possible causes: - Misaligned structures - Wrong reference frame - Including flexible loops

Solutions: - Enable alignment option - Try different reference frames - Use more specific atom selection (e.g., secondary structure only)

Issue: Choppy or discontinuous plots¶

Possible causes: - Files not in correct order - Time assignment incorrect - Missing frames

Solutions: - Reorder files using drag-and-drop - Verify time assignments - Check trajectory files for completeness

Issue: Energy values seem wrong¶

Possible causes: - Wrong units selected - Log files not from same simulation - Parsing errors

Solutions: - Check unit selection (kcal/mol vs kJ/mol) - Verify log files are sequential - Check status messages for warnings

Issue: Memory errors with large trajectories¶

Solutions: - Analyze in smaller chunks - Use more specific atom selections - Increase system RAM - Close other applications

Best Practices¶

For Structural Analysis¶

1. Always check alignment: Enable for RMSD calculations
2. Use appropriate selections: Backbone for overall structure, C-alpha for simplicity
3. Verify time assignments: Especially for concatenated trajectories
4. Export data regularly: Don't lose analysis results
5. Check convergence: RMSD should plateau

For Energetic Analysis¶

1. Sequential file ordering: Equilibration → Production phases
2. Assign times accurately: Match actual simulation times
3. Plot multiple properties: Check system stability
4. Monitor temperature: Should be stable (±1-2 K)
5. Check energy drift: Total energy should be conserved (NVE) or stable (NVT/NPT)

For Publication¶

1. Use consistent units: Pick one set and stick to it
2. Export high-resolution plots: SVG for vector graphics
3. Save raw data: CSV or NumPy for later analysis
4. Document parameters: Note selections, reference frames, etc.
5. Check error bars: Consider statistical analysis of multiple runs

Example Workflows¶

Workflow 1: Basic RMSD Analysis¶

1. Load topology: system.psf
2. Add trajectory: production.dcd
3. Assign time: 100 ns
4. Select: RMSD analysis
5. Atom selection: protein and name CA
6. Reference frame: 0
7. Enable alignment: Yes
8. Run analysis
9. Export: plot as PNG, data as CSV

Workflow 2: Multi-File Energy Analysis¶

1. Add files:
   - min.log → 0.1 ns
   - equil.log → 1.0 ns
   - prod1.log → 50 ns
   - prod2.log → 50 ns
2. Total timeline: 0-101.1 ns
3. Select properties: TOTAL, TEMP, PRESSURE
4. Units: X=ns, Y=kcal/mol
5. Run analysis
6. Export: data as JSON

Workflow 3: Residue Flexibility¶

1. Load topology and trajectory
2. Select: RMSF analysis
3. Atom selection: protein and name CA
4. Run analysis
5. Identify flexible regions (RMSF > 2 Å)
6. Cross-reference with structure
7. Export: plot and data

For more examples and detailed tutorials, see the User Guide.