Pauling runs GROMACS under the hood -- same engine, same force fields, same physics -- but handles the entire pipeline automatically, from PDB to production trajectory, with automatic ligand parameterization and MM-PBSA. GROMACS itself is the gold standard for molecular dynamics -- fast, free, incredibly capable -- but incredibly manual: topology files, .mdp configs, pdb2gmx, solvation, ion addition, equilibration. A full day of expert setup per simulation.
| Category | Pauling | GROMACS |
|---|---|---|
| MD engine | GROMACS (same engine) | GROMACS |
| Force fields | AMBER, CHARMM, OPLS via GROMACS | AMBER, CHARMM, OPLS, GROMOS, custom |
| Simulation physics | Identical -- same integrators, PME, constraints | Full control over every parameter |
| Setup complexity | Conversational: describe your system, get a running simulation | Manual: pdb2gmx, editconf, solvate, genion, grompp, mdrun |
| Ligand parameterization | Automatic via ACPYPE -- topology and charges generated from SMILES or SDF | Manual: ACPYPE/CGenFF/GAFF outside GROMACS, then merge topologies by hand |
| Checkpoint & resume | Built-in save/resume with automatic state management | Native .cpt files, but you manage restarts and file paths manually |
| GPU acceleration | Cloud GPUs provisioned automatically -- no hardware to manage | Excellent GPU kernels, but you provision and configure the hardware |
| Cloud scaling | Google Cloud Dataflow with Apache Beam -- auto-scales to hundreds of workers | No cloud integration -- you manage HPC queues or cloud VMs yourself |
| Pipeline integration | Docking, pocket detection, ADMET, QC all in one workflow | MD only -- you stitch together separate tools for a full pipeline |
| Learning curve | Conversational interface -- describe what you want in plain language | Steep: weeks to months to become proficient with config files and workflows |
| Customization | Curated defaults with parameter overrides | Full control over every .mdp parameter and simulation detail |
| Cost | Pay-per-use cloud compute, no license | Free and open source, but you pay for hardware and sysadmin time |