Molecular Dynamics Analysis
Made Simple

Upload your topology & trajectory files and get publication-quality plots in minutes. No scripting required.

RMSDRMSF Radius of GyrationFree Energy Landscape Binding EnergyP-L Distance

Run Analysis

1 Upload Files

📄

Topology File

PDB · GRO

Drag & drop or click to browse

🎞️

Trajectory File

XTC · TRR · DCD

Drag & drop or click to browse

2 Selections (optional)

Protein Selection

Ligand Selection

Timestep Override (ps) — 0 = auto

Temperature (K)

3 Choose Analyses

RMSD RMSF Radius of Gyration Free Energy Landscape Binding Energy P-L Distance

Extract a specific conformation from your trajectory as a PDB file.

Provide a topology (PDB/GRO) and trajectory (XTC/TRR/DCD). Compatible with GROMACS, AMBER, CHARMM, and NAMD.

Set your selection strings, optional timestep override, and choose which analyses to run.

The tool runs MDAnalysis server-side and computes RMSD, RMSF, Rg, FEL, Binding Energy, and P-L Distance.

View publication-quality plots (300 DPI) directly in the browser and download all as a ZIP.

Topology Formats

PDB GRO PSF TOP

Trajectory Formats

XTC TRR DCD NetCDF

MD Engines

GROMACS AMBER CHARMM NAMD