Run production-scale molecular dynamics without managing GPUs
Production MD runs on the engine's GPUs, so a small team gets the same simulation a large pharma does. 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 GPU. 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, past a single static score
Evaluate protein flexibility and conformational dynamics
Prioritize candidates before committing to experiments
Run membrane protein simulations, setup handled for you
Validate candidates in silico, before the lab
GROMACS on GPU. MM-GBSA binding energy. Identify unstable candidates computationally.