How to Use Our Tools

Interactive guides for each tool. Switch between tutorials to learn step-by-step. Click elements to highlight and explore.

MD Simulation Plotter Guide

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

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

Simulation File Upload

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

Configure frame range, selection

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

Configure Analysis

Select analysis metric and parameters

Metric: RMSDSelection: protein

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

Run Analysis

Click to start MD analysis

Metric: RMSDFrames: 1000

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

Analysis Results

Frame	RMSD (Å)
1	0.123
2	0.145

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

•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

RMSD Plot Preview

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

Download Image

Choose a tool above and follow the steps to create stunning visualizations. It's intuitive and powerful!