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.

How the stack fits together

Conda environments manage Python dependencies. They do not need to own the system GROMACS installation. In the companion workstation workflow, all environments should still call /usr/local/bin/gmx.

System

GROMACS

/usr/local/bin/gmx

Conda

cgenff

Preparation and parameterization dependencies

Conda

mdanalysis

Trajectory analysis and plotting dependencies

/usr/local/bin/gmx
cgenff mdanalysis future environments

PyMACS uses the Conda environments for Python packages while keeping the simulation engine independent and shared.

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

Verify GROMACS visibility

Run these checks after environment creation and again if a later package install changes which gmx executable is active.

  • gmx --version confirms that GROMACS is callable.
  • which gmx shows the active executable that your shell will use first.
  • type -a gmx shows every visible gmx on PATH and helps diagnose Conda shadowing.
Copy command 
which gmx
gmx --version
type -a gmx
See GROMACS installation

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.