Introduction

OpenFF Interchange is a Python package developed by the Open Force Field Initiative for storing, manipulating, and converting molecular mechanics data. The package is oriented around the Interchange class, which stores a molecular mechanics system and provides methods to write the system out in numerous formats.

An Interchange contains a fully parameterized molecular system with all the information needed to start a simulation. This includes the force field, box vectors, positions, velocities, and a topology containing individual molecules and their connectivity. For most users, Interchange forms the bridge between the OpenFF ecosystem and their simulation software of choice; users describe their system with the OpenFF Toolkit and then parameterize it with Interchange.

An Interchange stores parameters in classes that link the topology to the force field. This allows changes in the force field to be reflected in the Interchange immediately. This is useful for iteratively tweaking parts of a force field without having to recompute expensive parts like the charges.

Once the Interchange is created and parameterized, it can be exported as simulation-ready input files to a number of molecular mechanics software packages, including Amber, OpenMM, GROMACS, and LAMMPS.

--- alt: "Flowchart describing the construction and use of an Interchange (See textual description below)" align: center --- flowchart LR OFFXML SMILES/SDF/PDB BoxVecs[Box vectors] Positions Velocities subgraph tk [openff.toolkit] Molecule([Molecule]) ForceField([ForceField]) end subgraph int [openff.interchange] Interchange[(Interchange)] FromSmirnoff[["from_smirnoff()"]] end GMX{{GROMACS}} CHARMM{{CHARMM}} Amber{{Amber}} OpenMM{{OpenMM}} LAMMPS{{LAMMPS}} style tk fill:#2f9ed2,color:#fff,stroke:#555; style int fill:#ee4266,color:#fff,stroke:#555; classDef default stroke:#555; classDef code font-family:cousine,font-size:11pt,font-weight:bold; class FromSmirnoff,Molecule,ForceField,Interchange,tk,int code OFFXML --> ForceField --> FromSmirnoff SMILES/SDF/PDB --> Molecule --> FromSmirnoff FromSmirnoff --> Interchange BoxVecs -..-> Interchange Positions -..-> Interchange Velocities -..-> Interchange Interchange --> Amber Interchange --> OpenMM Interchange -.-> GMX Interchange -.-> CHARMM Interchange -.-> LAMMPS

Interchange’s goals

OpenFF Interchange aims to provide a robust API for producing identical, simulation-ready systems for all major molecular mechanics codes with the Open Force Field software stack. Interchange aims to support systems created with the OpenFF Toolkit, which can be converted to Interchange objects by applying a SMIRNOFF force field from the Toolkit or a Foyer force field. The Interchange object can then produce input files for downstream molecular mechanics software suites. At present, it supports Amber and OpenMM. GROMACS, and LAMMPS support is in place but experimental, and support for CHARMM is planned.

By design, Interchange supports extensive chemical information about the target system. Downstream MM software generally requires only the atoms present in the system and the parameters for their interactions, but Interchange additionally supports chemical information like their bond orders and partial charges. These data are not present in the final output, but allow the abstract chemical system under study to be decoupled from the implementation of a specific mathematical model. This allows Interchange to easily switch between different force fields for the same system, and supports a simple workflow for force field modification.

Converting in the reverse direction is a long term goal of the project.

Units in Interchange

As a best practice, Interchange always associates explicit units with numerical values. Units are tagged using the openff-units package, which provides numerical types associated with commonly used units and methods for ergonomically and safely converting between units. However, the Interchange API accepts values with units defined by the openmm.units or unyt packages, and will automatically convert these values to the appropriate unit to be stored internally. If raw numerical values without units are provided, Interchange assumes these values are in the correct unit. Explicitly defining units helps minimize mistakes and allows the computer to take on the mental load of ensuring the correct units, so we highly recommend it.

Except where otherwise noted, Interchange uses a nm/ps/K/e/Da unit system commonly used in molecular mechanics software. This forms a coherent set of units compatible with SI:

Quantity

Unit

Symbol

Length

nanometre

nm

Time

picosecond

ps

Temperature

Kelvin

K

Electric charge

electron charge

e

Mass

Dalton

Da

Energy1

kilojoule/mol

kJ/mol
1

Derived unit