Pauling runs MD on cloud infrastructure without any cluster management -- type what you want, get trajectories back, with docking, ADMET, and QC in the same workflow. NAMD excels at large biomolecular systems -- scalable, well-optimized for HPC clusters, strong in membrane simulations -- but it requires cluster access, CHARMM-GUI for setup, and significant HPC expertise.
| Category | Pauling | NAMD |
|---|---|---|
| MD engine | GROMACS (GPU-accelerated, widely validated) | NAMD (Charm++, designed for massive parallelism) |
| Large system performance | Cloud GPU scaling -- handles large systems without HPC queues | Best-in-class scaling for multi-million atom systems across thousands of cores |
| Membrane simulations | Supported via GROMACS with automated setup | Strong: tight CHARMM-GUI integration for complex membrane systems |
| HPC scaling | Auto-scaling on Google Cloud Dataflow -- no cluster management | Exceptional: scales to tens of thousands of CPU cores on HPC clusters |
| Cloud infrastructure | Native: Google Cloud with Apache Beam, managed storage, auto-provisioning | No cloud layer -- you deploy on HPC clusters or self-managed VMs |
| Setup complexity | Conversational: describe the system, get production MD | NAMD config files + CHARMM-GUI or VMD for system preparation |
| Force fields | AMBER, CHARMM, OPLS via GROMACS | CHARMM, AMBER (via chamber), OPLS -- strong CHARMM ecosystem |
| Ligand parameterization | Automatic via ACPYPE from SMILES or SDF | CGenFF via CHARMM-GUI or ParamChem -- manual but well-documented |
| Pipeline integration | Full drug discovery: docking (UniDock), pocket detection (P2Rank), ADMET, QC | MD-focused; separate tools needed for docking, ADMET, pocket detection |
| Steered MD / Enhanced sampling | Standard MD with MM-PBSA binding energy validation | Excellent: SMD, ABF, metadynamics via colvars -- strong enhanced sampling toolkit |
| Learning curve | Conversational interface -- no config files or HPC knowledge needed | Moderate: config files are readable, but HPC deployment adds complexity |
| Cost | Pay-per-use cloud compute, no license | Free for academic use; commercial license required for industry |