Design Principles

Scope and Features of GMSO

GMSO is designed to enable the flexible, general representation of chemical topologies for molecular simulation. Efforts are made to enable lossless, bias-free storage of data, without assuming particular chemistries, models, or using any particular engine’s ecosystem as a starting point. The scope is generally restrained to the preparation, manipulation, and conversion of and of input files for molecular simulation, i.e. before engines are called to execute the simulations themselves. GMSO currently does not support conversions between trajectory file formats for analysis codes. In the scope of molecular simulation, we loosely define a chemical topology as everything needed to reproducibly prepare a chemical system for simulation. This includes particle coordinates and connectivity, box information, force field data (functional forms, parameters tagged with units, partial charges, etc.) and some optional information that may not apply to all systems (i.e. specification of elements with each particle).

GMSO enables the following features:

  • Supporting a variety of models in the molecular simulation/computational chemistry community: No assumptions are made about an interaction site representing an atom or bead, instead supported atomistic, united-atom/coarse-grained, polarizable, and other models!
  • Greater flexibility for exotic potentials: The AtomType (and analogue classes for intramolecular interactions) uses sympy to store any potential that can be represented by a mathematical expression. If you can write it down, it can be stored!
  • Easier development for glue to new engines: by not being designed for compatibility with any particular molecular simulation engine or ecosystem, it becomes more tractable for developers in the community to add glue for engines that are not currently supported (and even ones that do not exist at present)!
  • Compatibility with existing community tools: No single molecular simulation tool will be a silver bullet, so GMSO includes functions to convert objects. These can be used in their own right to convert between objects in-memory and also to support conversion to file formats not natively supported at any given time. Currently supported conversions include ParmEd, OpenMM, mBuild, MDTraj, with others coming in the future!
  • Native support for reading and writing many common file formats (XYZ, GRO, TOP, LAMMPSDATA) and indirect support, through other libraries, for many more!

Structure of GMSO

There are three main modules within the Python package:

  • gmso.core stores the classes that constitute the core data structures.
  • gmso.formats stores readers and writers for (on-disk) file formats.
  • gmso.external includes functions that convert core data structures between external libraries and their internal representation.