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Installation

Requirements

  • Python 3.10-3.14

Core dependencies are handled automatically by pip, including RDKit and the upstream PACKMOL package and executable. See requirements.txt.

Installing mdinterface

pip install mdinterface

git clone https://github.com/roncofaber/mdinterface.git
cd mdinterface
pip install -e .

Optional extras

pip install mdinterface[resp]   # RESP charge analysis (PySCF / gpu4pyscf)
pip install mdinterface[aimd]   # FAIRChem AIMD
pip install mdinterface[all]    # everything

LigParGen (automatic OPLS-AA parameters)

Install the mdinterface-compatible LigParGen fork in the same environment, then verify that its command is available:

python -m pip install "git+https://github.com/roncofaber/ligpargen.git@ad78036842318f166531be41cfcbc3563d7c5476"
conda install -c conda-forge openbabel
ligpargen -h
obabel -V

The pinned revision includes chemistry-preserving atom reordering required for RDKit-backed inputs. Those inputs use MOL files to preserve explicit bonds and formal charges. Open Babel is required for coordinate-only ASE inputs, which use XYZ files.

LigParGen requires BOSS, a 32-bit binary. Point mdinterface to it via BOSSdir in the config file. Three modes are supported depending on how BOSS is available:

The configuration file is read when LigParGen is invoked. An existing BOSSdir environment variable takes precedence over the file value.

Build the container with boss-container, then:

# ~/.config/mdinterface/config.ini
[settings]
BOSSdir = /path/to/boss-container.sif

Build the container with boss-container, then:

# ~/.config/mdinterface/config.ini
[settings]
BOSSdir = boss-container:latest

Requires csh installed on the host and a working 32-bit BOSS binary:

# ~/.config/mdinterface/config.ini
[settings]
BOSSdir = /path/to/boss

The boss-container repository contains only build recipes. Each user must supply a licensed BOSS installation when building an image. A built Docker image, exported archive, or Apptainer file contains BOSS and must remain private unless the license explicitly permits sharing it.

The container supplies the 32-bit userspace libraries that are commonly missing on modern x86-64 Linux systems. Because Docker and Apptainer share the host kernel, they do not by themselves solve an unsupported CPU architecture, a kernel without the 32-bit x86 ABI, or a security policy that blocks the required system calls.

Full parameterization development environment

Use the checked-in environment definition when developing LigParGen or the planned OpenFF integration:

mamba env create -f environment-full.yml
mamba activate mdinterface-full

This installs Python 3.12, the local mdinterface checkout, the mdinterface-compatible LigParGen fork, Open Babel, AmberTools, OpenFF Toolkit and Interchange, CPU-only NAGL and PyTorch, PACKMOL, the test suite, and documentation tooling. The full environment uses Python 3.12 and NumPy 1.x to satisfy the current AmberTools dependency stack, while the core mdinterface package continues to support Python 3.10-3.14. BOSS is not included and must still be configured through BOSSdir.

If LigParGen is cloned next to mdinterface, replace the installed Git version with the local checkout for development:

python -m pip install -e ../ligpargen

OpenFF 2.2.1 parameterization has been validated through AmberTools, and OpenFF 2.3 has been validated through CPU-only NAGL on Python 3.14. OpenFF-to-LAMMPS export and mdinterface import have also been validated. OpenFF is not yet a supported Specie backend because mdinterface must first preserve Fourier torsion styles, mixing rules, switching behavior, and 1-4 scaling metadata across assembly and output.

RESP charges with PySCF

Install PySCF and PyMBXAS. RESP fitting currently requires gpu4pyscf.

AIMD with FAIRChem

pip install fairchem-core