PyMACS documentation
The README, rebuilt as clickable website pages.
These pages follow the detailed PyMACS README but organize it for pymacs.com. Use the docs when you need installation, environments, force fields, CGenFF, run templates, flags, analysis outputs, restarts, examples, or troubleshooting.
Install PyMACS and create a clean working folder
Use this page when you need PyMACS files in a fresh directory and want the safest path before running the examples.
OrientationRepository 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.
SetupSystem requirements and environments
PyMACS expects a Python environment, GROMACS, and the correct setup and analysis dependencies. Most users should keep setup and analysis environments separate.
StructuresSupported inputs and structure preparation
PyMACS can start from local structural files or fetch structures from the PDB. The important beginner skill is knowing what the selected input contains.
PhysicsForce fields included in PyMACS
The force field defines the classical physics model used by the simulation. PyMACS centers CHARMM-family workflows and ships both standard and LJ-PME-compatible CHARMM folders.
LigandsLigand parameterization and CGenFF support
Small molecules need parameters that agree with the biomolecular force field. PyMACS supports practical CGenFF workflows while keeping ligand names and topology files aligned.
RecipesQuick start templates for real run folders
The README contains repeatable run-folder templates. The website version separates them into workstation, MPI/HPC, and analysis-only patterns.
PipelinePipeline stages and what each script does
The PyMACS scripts are numbered because each one answers a different scientific and operational need.
ReferenceCommand-line flags and beginner-safe defaults
PyMACS exposes many controls, but most first runs only need a small set of flags. This page groups the important ones by decision type.
RecoveryRestarting and resuming production MD
Long simulations can be interrupted. PyMACS supports checkpoint-aware restart behavior so users do not have to throw away completed work.
InterpretationAnalysis outputs and interaction definitions
PyMACS translates raw trajectories into plots, CSV tables, networks, and figurebooks. The goal is not just to produce files, but to make the simulation interpretable.
ExamplesCurated examples and Git LFS
The repository includes examples for protein-ligand, cofactor-aware, biological assembly, and PROTAC workflows. Large example assets may require Git LFS.
DebuggingTroubleshooting common PyMACS problems
Most first failures are caused by environment, folder, input-file, ligand-name, or topology mismatches. Check the simple things before changing scientific settings.
JudgmentBest practices, provenance, and citation
PyMACS automates the workflow, but users still need scientific judgment. This page collects the practices that make runs easier to trust and easier to explain.