Binding-energy assessment with molecular dynamics

Short MD · MM/PBSA

Upload a protein complex, relax it with short molecular dynamics, and estimate receptor–ligand interaction energy in one workspace.

New binding-energy run

Required fields first. Advanced execution controls stay out of the way until you need them.

01Input|Add the starting structure

Coordinates are validated in your browser before submission.

Drop a PDB here, or browse files.pdb or .ent · up to 20 MiBChoose file

Advanced settings

Execution mode

Run name

Energy analysis start · optional

Leave blank to detect a stable RMSD tail. A manual value overrides that window and is recorded in the result.

Amber99SB-ILDN · TIP3P water · 0.15 M salt · 2 fs timestep. Automatic plateau calls require at least 1 ns; shorter runs remain technical checks.

Recent binding-energy runs

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