GMSO: Flexible storage of chemical topology for molecular simulation

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GMSO is a flexible storage of chemical topology for molecular simulation. With a few lines of GMSO code, together with mBuild and foyer, users can rapidly prototype arbitrary parameterized chemical systems and generate data files for a wide variety of simulation engines.

GMSO is a part of the MoSDeF ecosystem

GMSO is designed to be a general and flexible representation of chemical topologies for molecular simulation. With an emphasis on assuming as little as possible about the chemical system, model, or engine, GMSO can enable support for a variety of systems.

GMSO is a part of the MoSDeF (Molecular Simulation and Design Framework) ecosystem, and is intended to be a generalized alternative for the foyer package. Libraries in the MoSDeF ecosystem are designed to provide utilities necessary to streamline a researcher’s simulation workflow. When setting up simulation studies we also recommend users follow the TRUE (Transparent, Reproducible, Usable-by-others, and Extensible) standard.

Goals and Features

GMSO’s goal is to provide a flexible backend framework to store topological information of a chemical system in a reproducible fashion. Topology in this case is defined as the information needed to initialise a molecular simulation. Depending on the type of simulation performed, this ranges from:

  • particle positions

  • particle connectivity

  • box information

  • forcefield data

    • functional forms defined as sympy expressions

    • parameters with defined units

    • partial charges

    • tabulated data

    • etc.

  • Other optional data

    • particle mass

    • elemental data

With these driving goals for GMSO, the following features are enabled:

  1. Supporting a variety of models: no assumptions are made about an interaction site representing an atom or bead — these can be atomistic, united-atom/coarse-grained, polarisable, and other models.

  2. Greater flexibility for exotic potentials: AtomType (and analogous classes for intramolecular interactions) uses sympy to store any potential that can be represented by a mathematical expression.

  3. Adaptable for new engines: by not being designed for compatibility with any particular simulation engine, it is more tractable for community developers to add support for engines not currently supported.

  4. Compatibility with existing community tools: GMSO includes functions to convert between various file formats and libraries. Currently supported conversions include:

    • ParmEd

    • OpenMM

    • mBuild

    • HOOMD-blue

    • NetworkX

  5. Native support for reading and writing many common file formats:

    • XYZ

    • GRO / TOP / ITP

    • LAMMPS DATA

    • GSD

    • MOL2

    • MCF

    • JSON