Orientation

Repository map and what each folder is for

PyMACS includes scripts, templates, force fields, curated examples, documentation, and analysis assets. Knowing the folder layout prevents many beginner mistakes.

Main project files

Path	Purpose
1_AutomateGromacs.py	System setup, topology generation, box, solvation, ions, and EM input.
2_AutomateGromacs.py	Energy minimization, NVT, NPT, production MD, CPU/GPU controls, and restarts.
3A_AutomateGromacs.py	Trajectory processing, RMSD/RMSF/Rg, contacts, interaction summaries, and mode routing.
3B_NETWORX.py	Ligand-residue or peptide-contact network rendering.
3C_Interface_RIN.py	Protein-protein or protein-peptide interface residue interaction networks.
3_PROTAC_Analysis.py	Dedicated ternary-complex and PROTAC analysis.
4PDF4MD.py	Figurebook assembly from generated analysis plots.

Folders users should recognize

Folder	What it contains
MDPs/	GROMACS parameter templates for EM, NVT, NPT, and production MD.
charmm36.ff/	Standard CHARMM36-family force-field folder.
charmm36_ljpme-jul2022.ff/	CHARMM36-compatible LJ-PME force-field folder.
Example_Choices/	Curated example systems and reference outputs.
docs/	Supporting notes, output-gallery documentation, and citation guidance.
Analysis_Results/	Generated analysis outputs created after a run.

Beginner rule

Do not edit force-field folders, MDP templates, generated topology files, or packaged example outputs until you understand why that edit is necessary. Copy examples into a fresh RUNS folder instead.