Setup

System 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.

Required tools

  • Python for running the PyMACS automation scripts.
  • GROMACS for topology processing, minimization, equilibration, production MD, and trajectory conversion.
  • Conda or another environment manager for repeatable dependencies.
  • Git and Git LFS when cloning the full repository and curated example assets.

Recommended Conda environments

Copy command 
conda env create -f environment_cgenff.yml
conda env create -f environment_mdanalysis.yml

conda activate cgenff
python 1_AutomateGromacs.py --help

conda activate mdanalysis
python 2_AutomateGromacs.py --help
python 3A_AutomateGromacs.py --help

Non-Conda fallback

Advanced users can use a Python virtual environment, but they must still make GROMACS and any force-field or ligand-conversion tools visible on PATH.

Copy command 
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -r requirements.txt
gmx --version

Pre-repairing structures

If PyMACS cannot repair a deposited structure cleanly, prepare the protein or biological assembly first with a dedicated structure-repair tool, then give the repaired file to Script 1.