BioSimSpace is an interoperable Python framework for biomolecular simulation.

  • Read and write molecules from a number of molecular file formats. This includes AMBER, CHARMM, and GROMACS files.

  • Parameterise molecules using force fields from AmberTools and the Open Force Field Initiative.

  • Solvate molecules using a range of standard water models. We support both orthorhombic and triclinic simulation boxes.

  • Configure protocols for a range of biomolecular simulations and create processes to run them using our supported molecular dynamics (MD) engines ( AMBER, GROMACS, OpenMM, NAMD, SOMD).

  • Setup and run free energy perturbation simulations with SOMD and GROMACS. (See our hydration free energy tutorial for a complete example.)

  • Configure and run metadynamics simulations for a range of supported collective variables. (See our tutorial for a complete example.)

  • Write interoperable workflow components or nodes that work with any supported MD engine and can be run from the command-line, within a Jupyter notebook, or exported to a Common Workflow Language Tool wrapper.

  • Interact with molecular simulation process within interactive Python environments. This includes: starting and stopping simulations, monitoring their progress, getting time series data of thermodynamic state information, plotting data, analysing trajectories, and visualising molecules.