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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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MIT LicenseFollow Molly.jl
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