OpenMM MD

Prepare, solvate, and equilibrate protein structures with OpenMM (NVT or NPT Langevin).

System mode

Choose the type of molecular system.

Structure (PDB)

Enter a PDB ID (downloaded from RCSB) or upload a protein or protein complex in PDB format. The structure is sent as plain text in the job payload for preparation and solvation.

Equilibration uses Langevin dynamics in NVT or NPT. NPT requires explicit periodic solvent. Preparation uses the pH value for PROPKA protonation before solvation.

Optional MDAnalysis metrics comparing two partners (default chain A vs chain B). Includes CA RMSF, contact map, buried surface area, and center-of-mass distance.