SimLab Analyze
Upload an MD trajectory and get RMSD, RMSF, radius of gyration, hydrogen bonds, SASA, PCA, contacts, ligand interactions and MM/GBSA as publication-ready figures - no account needed.
What are you analysing?
Trajectory analysis
GROMACS tools
RMSD, RMSF, radius of gyration, hydrogen bonds, SASA, energy terms, PCA, free-energy landscape and contact maps from a structure and trajectory.
Open trajectory analysisInteractions
MDAnalysis
Protein–ligand systems: ligand RMSD, which residues hold the ligand (H-bonds, hydrophobic, ionic, water bridges), ProLIF interaction persistence over the run, and how its torsions evolve.
Open interaction analysisQuality checks
GROMACS energy + RMSD
Is the simulation equilibrated? Temperature, pressure, density, volume and energy drift against the run's own thermostat and barostat targets, plus an RMSD plateau test - one verdict per check.
Open quality checksCompare systems
Completed runs
Overlay the same analysis across several runs - apo vs holo, mutants, or replicates with a mean ± SD band - and read the statistics side by side.
Open comparisonMM-GBSA
gmx_MMPBSA
Binding free energy from a protein–ligand trajectory with per-term breakdown and per-residue decomposition. Needs the .tpr and the topology bundle.
Open MM-GBSAPlot files
In your browser
Already have .xvg or .csv output? Drop the files for publication-style figures, overlays and exports. Nothing is uploaded or stored.
Open the plotterNo account needed. Have a job code from an earlier run? Retrieve it here.