Much of science can be explained by the movement and interaction of molecules. Molecular dynamics (MD) is a computational technique used to explore these phenomena, from noble gases to biological macromolecules. Molly.jl is a pure Julia package for MD, and for the simulation of physical systems more broadly. The package is described in a talk at Enzyme Conference 2023 and an earlier talk at the JuliaMolSim minisymposium at JuliaCon 2022. Slides are also available for a tutorial in September 2023.

Features

  • Non-bonded interactions
  • Bonded interactions
  • Interface to allow definition of new interactions, simulators, thermostats, neighbor finders, loggers etc.
  • Verlet, velocity Verlet, Störmer-Verlet, flexible Langevin and Nosé-Hoover integrators
  • Andersen, Berendsen and velocity rescaling thermostats
  • Periodic, triclinic and infinite boundary conditions
  • Flexible loggers to track arbitrary properties throughout simulations

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License

MIT License

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Additional Project Details

Programming Language

Julia

Related Categories

Julia Data Visualization Software

Registered

2023-11-10