QTRAP — automated QM/MM dynamics workflow
2026 · Research toolQuantum mechanics/molecular mechanics Trajectory Running, Analysis, and Preprocessing: a workflow that automates quasiclassical QM/MM dynamics simulations end to end. It has two parts — a ten-step preprocessing and execution pipeline that turns a raw molecular dynamics trajectory into completed QM/MM runs on an HPC cluster, and an agentic layer that lets an AI agent run the whole procedure interactively or independently with minimal user input.
- As far as I could find, no automated workflow for quasiclassical QM/MM dynamics had been published before this one.
- Handles the full path from a NetCDF trajectory to per-residue RMSD, reaction-coordinate tracking, and partial decomposition analysis.
- Ships with source code, worked examples, documentation, and scaffolding so the workflow is reproducible by someone who didn't write it.
- Designed for femtosecond-scale dynamics in ligand–receptor systems, where the underlying method is powerful but rarely used because the setup cost is so high.
Skills applied