Pauling gives you MD through conversation on managed cloud GPUs -- same class of physics, no code, with docking, ADMET, and QC in the same workflow. OpenMM is a Python-native MD engine -- flexible, GPU-accelerated, great for custom workflows and ML integration -- but you're writing Python scripts for every simulation, managing your own GPU hardware, and building the pipeline from scratch.
| Category | Pauling | OpenMM |
|---|---|---|
| MD engine | GROMACS (compiled C++/CUDA, highly optimized) | OpenMM (Python API over C++/CUDA kernels) |
| Python API | Not required -- conversational interface handles everything | First-class Python API -- build simulations programmatically with full control |
| ML potential integration | Physics-based force fields (AMBER, CHARMM, OPLS) | Excellent: ANI, MACE, SchNet plug directly into the simulation loop via OpenMM-ML |
| GPU acceleration | Cloud GPUs provisioned automatically -- no CUDA setup | Strong GPU performance, but you install CUDA, manage drivers, and allocate hardware |
| Cloud infrastructure | Google Cloud Dataflow with Apache Beam -- auto-scaling to hundreds of workers | No cloud layer -- you deploy on your own machines or write cloud orchestration code |
| Setup & scripting | Zero code: describe your simulation in natural language | Python scripting required for every simulation; flexible but time-consuming |
| Force fields | AMBER, CHARMM, OPLS via GROMACS | AMBER, CHARMM, OPLS, plus easy custom force field definition in Python |
| Ligand parameterization | Automatic via ACPYPE -- topology and charges from SMILES or SDF | Manual: OpenFF Toolkit, GAFF via ParmEd, or custom XML force field files |
| Pipeline integration | Full drug discovery: docking (UniDock), pocket detection (P2Rank), ADMET, QC (MolProbity, PoseBusters) | MD only -- you integrate docking, ADMET, and QC tools yourself |
| Checkpoint & resume | Automatic state saving and resume across cloud workers | Native checkpointing via Simulation.saveCheckpoint(), but you manage the logic |
| Extensibility | Curated pipeline with parameter overrides | Unlimited: custom forces, integrators, reporters -- anything expressible in Python |
| Cost | Pay-per-use cloud compute, no license | Free and open source, but you pay for GPU hardware and engineering time |