Most small biotech teams don't have — the GPU infrastructure
Without GPU provisioning, GROMACS setup, trajectory parsing, or a separate MM-GBSA step. Submit a protein-ligand complex. The platform handles force field selection, solvation, equilibration, production, and analysis — on GPU.
“Run a 10ns MD simulation of this protein-ligand complex and calculate MM-GBSA binding free energy.”
How it works
Submit a PDB ID or complex
Provide a protein PDB ID, duration, and temperature. The audit_system pre-flight classifier detects membrane proteins, metal sites, and heme clusters — routing complex cases to the appropriate pipeline or AlphaFlow.
Production MD on GPU
GROMACS runs on Azure GPUs. Soluble proteins use AMBER99SB-ILDN. Membrane proteins use CHARMM36m via packmol-memgen. Metalloprotein parameters via MCPB.py. Jobs run async — minutes to hours depending on system size.
Structured results returned
RMSD convergence, RMSF flexibility, radius of gyration, hydrogen bond analysis, equilibration assessment (temperature, pressure, density, energy). MM-GBSA binding free energy. Full trajectory data with interactive charts.
Proof
GROMACS 2023.3 on Azure Container Apps GPU. OpenFF Sage 2.x force fields. PACKMOL-Memgen for membrane systems.
audit_system pre-flight: OPM membrane detection, metal site coordination geometry, heme/Fe-S cluster identification. Routes complex cases to AlphaFlow automatically.
parameterize_metal: QM→FF bridge via MCPB.py for metalloprotein MD. Async jobs with email notifications on completion via Resend.
Dynamics, not snapshots
GROMACS on GPU. MM-GBSA. Async results. Sign up and run your first simulation.