GMSO: General Molecular Simulation Object
GMSOis a flexible storage of chemical topology for molecular simulation.
With a few lines of
GMSO code, together with
foyer, users can rapidly prototype arbitrary parameterized chemical systems and generate data files for a wide variety of simulation engines.
To learn more, get started, or contribute, check out our Documentation.
GMSO within the MoSDeF Ecosystem
import foyer from mbuild.lib.molecules import Ethane from gmso.external.convert_parmed import from_parmed from gmso.formats.lammpsdata import write_lammpsdata # Start with a mBuild compound mb_ethane = Ethane() oplsaa = foyer.Forcefield(name='oplsaa') # atomtype the system with foyer, and convert the resulting structure to a topology typed_ethane = from_parmed(oplsaa.apply(mb_ethane)) typed_ethane.name = 'ethane' # Write out lammps datafile write_lammpsdata(typed_ethane, filename='ethane.lammps', atom_style='full')
GMSO is designed to be a general and flexible representation of chemical topolgies 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 the backend replacement for the
Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline
a researcher's simulation workflow. When setting up simulation studies,
we also recommend users to follow the TRUE
(Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common
practices meant to improve the reproducibility of computational simulation research.
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 initialize 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
- parameters with defined units
- partial charges
- tabulated data
- functional forms defined as
- Other optional data
- particle mass
- elemental data
With these driving goals for
GMSO, the following features are enabled:
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 these can be atomistic, united-atom/coarse-grained, polarizable, and other models!
Adaptable for 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.
Compatibility with existing community tools: No single molecular simulation tool will ever be a silver bullet, so
GMSOincludes functions to convert between various file formats and libraries. 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:
Native support for reading and writing many common file formats: We natively have support for:
For full, detailed instructions, refer to the documentation for installation
conda installation quickstart
GMSO is available on
conda and can be installed as:
conda install -c conda-forge gmso
pip installation quickstart
GMSO is not on
pypi currently, but its dependencies are.
git clone https://github.com/mosdef-hub/gmso.git cd gmso pip install -r requirements.txt pip install -e .
pip quickstart will install
editable mode, which means that as you edit the source code of
GMSO those edits will be reflected in your installation.
The full documentation can be found at gmso.mosdef.org.