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MD Simulation Plotter Guide

Navigate through each step. Tap interactive elements to see highlights and tooltips.

Step 1: Upload Simulation Data

Upload molecular dynamics trajectory (e.g., DCD) and topology (e.g., PDB) files. Configure frame range and atom selection.

Key Details:

  • •Trajectory formats: DCD, XTC, TRR, NC
  • •Topology formats: PDB, GRO, PSF
  • •Max file size: 500MB for trajectory, 10MB for topology
  • •Settings: Frame range, atom selection (e.g., protein, backbone)

Simulation File Upload

Upload trajectory (e.g., DCD) and topology (e.g., PDB) files

Configure frame range, selection

Interactive Elements:

Step 2: Configure Analysis

Select analysis metric (e.g., RMSD, RMSF, Radius of Gyration, H-Bonds) and parameters like reference frame or residue selection.

Key Details:

  • •Metrics: RMSD, RMSF, Radius of Gyration, H-Bonds, SASA, Distance, Dihedral
  • •Reference: First frame or uploaded PDB
  • •Selections: Protein, backbone, specific residues, or atom groups
  • •Output: Per-frame or per-residue data

Configure Analysis

Select analysis metric and parameters

Metric: RMSDSelection: protein
Interactive Elements:

Step 3: Run Analysis

Run the selected MD analysis (e.g., RMSD calculation). Monitor progress with a loading indicator.

Key Details:

  • •Uses tools like MDAnalysis or GROMACS for computation
  • •Validates trajectory and topology compatibility
  • •Shows progress for large trajectories
  • •Errors for mismatched files or invalid selections

Run Analysis

Click to start MD analysis

Metric: RMSDFrames: 1000
Interactive Elements:

Step 4: View Results

Review analysis results in a table (e.g., RMSD per frame, RMSF per residue). Click rows for details.

Key Details:

  • •Table: Frame/residue number and metric value (e.g., RMSD in Å)
  • •Sortable by value or frame/residue
  • •Stats: Average, min, max, standard deviation
  • •Export: CSV with full data
Analysis Results
FrameRMSD (Å)
10.123
20.145
Interactive Elements:

Step 5: View Plots

View and download plots for RMSD, RMSF, Radius of Gyration, or H-Bonds. Switch between tabs to explore visualizations.

Key Details:

  • •Plots: RMSD (time vs Å), RMSF (residue vs Å), Radius of Gyration (time vs Å), H-Bonds (time vs count)
  • •High-resolution PNG output (1200x800)
  • •Downloadable with timestamped filenames
  • •Tabs to switch between plot types

MD Plots

RMSD Plot Preview

View RMSD, RMSF, Radius of Gyration, or H-Bonds plots

Plot

Download Image

Interactive Elements:

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