Create a clean run folder
Keep each system in its own directory so generated topologies, trajectories, CSV tables, plots, and logs stay reproducible.
mkdir -p RUNS/Example_CPD32 && cd RUNS/Example_CPD32Run PyMACS
A first-run path for new users.
The recommended first experience is the curated protein-ligand walkthrough. It shows the full rhythm of PyMACS without asking a new user to design a new simulation from scratch.
Before running
Know what needs to exist first.
PyMACS automates a difficult workflow, but the scientific inputs still matter. Start from a curated example, then change one thing at a time when moving to a new system.
GROMACS available on the machine or cluster where the simulation will run
The PyMACS repository files, including MDP templates and force-field folders
The cgenff environment for setup and ligand conversion
The mdanalysis environment for simulation control, analysis, plotting, and reports
Ligand CGenFF files when running ligand or cofactor systems
First run
Follow the workflow in order.
Prepare the system
Run Step 1 in the cgenff environment. This cleans the structure, builds topologies, places solvent and ions, and writes the energy-minimization input.
conda activate cgenff
python 1_AutomateGromacs.py --pdb CPD32_9G94.pdbRun equilibration and production
Run Step 2 in the analysis/simulation environment. This executes minimization, NVT, NPT, and production MD.
conda activate mdanalysis
python 2_AutomateGromacs.pyAnalyze the trajectory
Step 3A recenters the trajectory, calculates stability and flexibility metrics, extracts binding-pocket contacts, and prepares network-ready tables.
python 3A_AutomateGromacs.pyRender networks and reports
Step 3B creates ligand-residue network views when the required contact tables exist. Step 4 assembles the final figurebook.
python 3B_NETWORX.py
python 4PDF4MD.pyBefore production MD
The three stabilization stages.
Interpretation checks