Installation

FastMDXplora’s four phases have different dependency footprints. The analysis and report phases work from pip alone; the setup and simulation phases need PDBFixer and OpenMM, which are distributed primarily through conda-forge. Pick the route that matches what you need.

Full install (all four phases)

The setup and simulation chemistry stack (OpenMM, PDBFixer) installs most reliably from conda-forge, so the full install uses the bundled environment.yml. mamba is recommended (a faster conda solver); plain conda works too.

git clone https://github.com/aai-research-lab/FastMDXplora.git
cd FastMDXplora
mamba env create -f environment.yml || conda env create -f environment.yml
conda activate fastmdxplora
pip install -e .

Optional extras

pip install -e ".[ligand]"   # OpenFF small-molecule parameterization
pip install -e ".[plumed]"   # PLUMED enhanced sampling

The plumed extra also requires the openmm-plumed conda package:

conda install -c conda-forge openmm-plumed

Analysis and report only (from PyPI)

If you only need to analyze existing trajectories and build reports (no setup or simulation), plain pip is enough, with no conda required:

pip install fastmdxplora

The fastmdx command and import fastmdxplora are available either way. The short alias package fastmdx installs the same software:

pip install fastmdx

Verifying the install

fastmdx --version
python -c "import fastmdxplora; print(fastmdxplora.__version__)"

To check whether a GPU-capable OpenMM platform is available:

import openmm
plats = [openmm.Platform.getPlatform(i).getName()
         for i in range(openmm.Platform.getNumPlatforms())]
print("CUDA available" if "CUDA" in plats else "CPU-only; simulations will run on CPU")