Step 1
System Preparation
1_AutomateGromacs.py
Cleans the input structure, handles chains and components, prepares CHARMM-compatible topologies, solvates the system, adds ions, and produces a simulation-ready minimization input.
Open stepPyMACS workflow
Each script answers a different scientific need.
The numbered scripts are organized around the normal MD workflow: prepare a chemically valid system, simulate it, analyze the trajectory, visualize interactions, and assemble a report.
Step 2
Equilibration and Production MD
2_AutomateGromacs.py
Runs energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics with configurable MDP files and CPU/GPU resource controls.
Open stepStep 3A
Trajectory Analysis
3A_AutomateGromacs.py
Recenters trajectories, builds analysis-ready subsets, calculates RMSD/RMSF/Rg, detects contacts, classifies interaction behavior, and writes plots plus CSV tables.
Open stepStep 3B
Interaction Network Rendering
3B_NETWORX.py
Builds ligand-centered interaction diagrams that connect chemically drawn ligand atoms to nearby residues and interaction classes.
Open stepSpecialized
PROTAC and Ternary Complex Analysis
3_PROTAC_Analysis.py
Adds dedicated analysis for ternary-complex systems, including component-aware contacts, networks, geometry, quality-control manifests, and optional water bridges.
Open stepStep 4
Figurebook Generation
4PDF4MD.py
Compiles the plots, notes, contact summaries, and structural panels into a report-ready PDF figurebook.
Open step