Run production-scale molecular dynamics without managing GPUs
Most small biotech teams don't have the GPU infrastructure for MD - and shouldn't need it. Submit a protein-ligand complex. The engine handles force field selection, solvation, equilibration, production, and analysis. Identify unstable candidates before committing to lab validation.
“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 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.
Use this when you need to
Confirm binding stability over time - not just a static score
Evaluate protein flexibility and conformational dynamics
Prioritize candidates before committing to experiments
Run membrane protein simulations without CHARMM-GUI setup
Validate candidates before the lab - not after
GROMACS on GPU. MM-GBSA binding energy. Identify unstable candidates computationally.