Step 3A / 3A_AutomateGromacs.py
Trajectory Analysis
Recenters trajectories, builds analysis-ready subsets, calculates RMSD/RMSF/Rg, detects contacts, classifies interaction behavior, and writes plots plus CSV tables.
Why this step matters
A trajectory is only useful after it is translated into scientific questions: did the system stabilize, where did it fluctuate, and which contacts persisted?
Concepts to understand
Final_Trajectory exports
binding-pocket extraction
RMSD, RMSF, and radius of gyration
secondary structure persistence
ligand RMSD and ligand RMSF
contact cutoffs, hydrogen-bond-like events, and interaction summaries
Common outputs
Analysis_Results/Protein_RMSD.png
Analysis_Results/FullComplex_RMSD.png
Analysis_Results/Radius_of_Gyration_Overlay.png
Analysis_Results/*_Ligand_RMSD.png
Analysis_Results/FilteredContacts_Framewise.csv
Analysis_Results/InteractionTypes_Summary.csv
Typical commands
python 3A_AutomateGromacs.pypython 3A_AutomateGromacs.py --pocket-cutoff 6.0python 3A_AutomateGromacs.py --contact_cutoff 4.0 --hbond-distance-cutoff 3.5 --hbond-angle-cutoff 135