How nyelidl/pacs-q works
PaCS-Q runs parallel-cascade MD or QM/MM simulations: users provide topology, coordinates, settings and (for RMSD runs) a reference, then the CLI dispatches engine-specific runs. Each cycle analyzes candidate trajectories, selects a frame by RMSD or distance, and uses it to seed the next cycle; run outputs can be extended with rerun commands. The toolkit also includes trajectory analysis and QM-input generation capabilities documented in the README. Relationships shown here are limited to README statements and sampled source; analysis modules are present in the tree but their internal wiring was not sampled.
Main entry points: pacs_q_md.py MD CLI · pacsrmsd.py Frame selection · qmmm_setting.py Run settings · pacsq_run.py AMBER cascade
Components 26
Command entry
- QM/MM CLI
pacsq_toolkit/pacs_q.py - MD CLI
pacsq_toolkit/pacs_q_md.py - Input discovery
pacsq_toolkit/file_find.py
Cascade workflow
- AMBER cascade
pacsq_toolkit/pacsq_run.py - External QM run
pacsq_toolkit/pacsq_exq_run.py - QM/MM rerun
pacsq_toolkit/pacsq_rerun.py - OpenMM cascade
pacsq_toolkit/pacsq_openmm_run.py - OpenMM rerun
pacsq_toolkit/pacsq_openmm_rerun.py - PMEMD cascade
pacsq_toolkit/pacsq_pmemd_run.py - PMEMD rerun
pacsq_toolkit/pacsq_pmemd_rerun.py - Frame selection
pacsq_toolkit/pacsrmsd.py - Run settings
pacsq_toolkit/qmmm_setting.py
Simulation engines
- Sander MPI
pacsq_toolkit/sander_run_mpi.py - Sander
pacsq_toolkit/sander_run.py - PMEMD
pacsq_toolkit/pmemd_run.py - OpenMM
pacsq_toolkit/openmm_engine.py - AMBER
- OpenMM library
Analysis tools
- CV and 2D-PES
pacsq_toolkit/pacsana_dis_collection.py - MPI CV analysis
pacsq_toolkit/pacsana_dis_collection_mpi.py - PCA analysis
pacsq_toolkit/pacsana_procupine.py - QM input generation
pacsq_toolkit/pacsana_traj2orca.py - Gaussian inputs
pacsq_toolkit/pacsana_traj2g16.py - Parameter analysis
pacsq_toolkit/pacsana_3_para.py - MD trajectory
Other components
- Researcher
Connections 45
- Researcher → QM/MM CLI: invokes
README.md - Researcher → MD CLI: invokes
pacsq_toolkit/pacs_q_md.py - QM/MM CLI → Input discovery: finds inputs
pacsq_toolkit/pacs_q.py - MD CLI → Input discovery: finds inputs
pacsq_toolkit/pacs_q_md.py - MD CLI → AMBER cascade: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → External QM run: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → QM/MM rerun: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → OpenMM cascade: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → OpenMM rerun: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → PMEMD cascade: dispatches
pacsq_toolkit/pacs_q_md.py - MD CLI → PMEMD rerun: dispatches
pacsq_toolkit/pacs_q_md.py - AMBER cascade → Frame selection: selects frames
pacsq_toolkit/pacsq_run.py - External QM run → Frame selection: selects frames
pacsq_toolkit/pacsq_exq_run.py - QM/MM rerun → Frame selection: selects frames
pacsq_toolkit/pacsq_rerun.py - OpenMM cascade → Frame selection: selects frames
pacsq_toolkit/pacsq_openmm_run.py - OpenMM rerun → Frame selection: selects frames
pacsq_toolkit/pacsq_openmm_rerun.py - PMEMD cascade → Frame selection: selects frames
pacsq_toolkit/pacsq_pmemd_run.py - PMEMD rerun → Frame selection: selects frames
pacsq_toolkit/pacsq_pmemd_rerun.py - AMBER cascade → Run settings: writes settings
pacsq_toolkit/pacsq_run.py - External QM run → Run settings: reads settings
pacsq_toolkit/pacsq_exq_run.py - QM/MM rerun → Run settings: reads settings
pacsq_toolkit/pacsq_rerun.py - OpenMM cascade → Run settings: writes settings
pacsq_toolkit/pacsq_openmm_run.py - OpenMM rerun → Run settings: reads settings
pacsq_toolkit/pacsq_openmm_rerun.py - PMEMD cascade → Run settings: writes settings
pacsq_toolkit/pacsq_pmemd_run.py - PMEMD rerun → Run settings: reads settings
pacsq_toolkit/pacsq_pmemd_rerun.py - AMBER cascade → Sander MPI: runs candidates
pacsq_toolkit/pacsq_run.py - External QM run → Sander: runs candidates
pacsq_toolkit/pacsq_exq_run.py - QM/MM rerun → Sander MPI: extends runs
pacsq_toolkit/pacsq_rerun.py - OpenMM cascade → OpenMM: runs candidates
pacsq_toolkit/pacsq_openmm_run.py - OpenMM rerun → OpenMM: extends runs
pacsq_toolkit/pacsq_openmm_rerun.py - PMEMD cascade → PMEMD: runs candidates
pacsq_toolkit/pacsq_pmemd_run.py - PMEMD rerun → PMEMD: extends runs
pacsq_toolkit/pacsq_pmemd_rerun.py - PMEMD cascade → OpenMM: uses engine
pacsq_toolkit/pacsq_pmemd_run.py - OpenMM → OpenMM library: calls
pacsq_toolkit/openmm_engine.py - Sander MPI → AMBER: launches
pacsq_toolkit/sander_run_mpi.py - Sander → AMBER: launches
- PMEMD → AMBER: launches
- AMBER cascade → MD trajectory: produces
- OpenMM cascade → MD trajectory: produces
- Researcher → CV and 2D-PES: analyzes runs
README.md - Researcher → PCA analysis: analyzes runs
README.md - Researcher → QM input generation: generates inputs
README.md - Researcher → Gaussian inputs: generates inputs
- Researcher → MPI CV analysis: analyzes runs
- Researcher → Parameter analysis: analyzes runs