Molly.jl

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.

At the minute the package is a proof of concept for MD in Julia. It is not production ready, though it can do some cool things and is under active development. Implemented features include:

• Non-bonded interactions - Lennard-Jones Van der Waals/repulsion force, electrostatic Coulomb potential and reaction field, gravitational potential, soft sphere potential, Mie potential.
• Bonded interactions - covalent bonds, bond angles, torsion angles.
• Interface to allow definition of new interactions, simulators, thermostats, neighbor finders, loggers etc.
• Read in OpenMM force field files and coordinate files supported by Chemfiles.jl. There is also some support for Gromacs files.
• Andersen, Berendsen and velocity rescaling thermostats.
• Velocity Verlet and Störmer-Verlet integration.
• Periodic boundary conditions in a cubic box.
• Various neighbor list implementations to speed up calculation of non-bonded forces.
• Unitful.jl compatibility so numbers have physical meaning.
• Automatic multithreading.
• GPU acceleration on CUDA-enabled devices.
• Run with Float64 or Float32.
• Some analysis functions, e.g. RDF.
• Visualise simulations as animations.
• Physical agent-based modelling.
• Differentiable molecular simulation. This is a unique feature of the package and the focus of its current development.

Features not yet implemented include:

• Simulators such as energy minimisation, Langevin dynamics and REMD.
• Other temperature or pressure coupling methods.
• Protein preparation - solvent box, add hydrogens etc.
• Quantum mechanical modelling.
• High test coverage.
• API stability.

Installation

Julia is required, with Julia v1.7 or later required to get the latest version of Molly. Install Molly from the Julia REPL. Enter the package mode by pressing ] and run add Molly.

Usage

Some examples are given here, see the documentation for more on how to use the package.

Simulation of a Lennard-Jones fluid:

using Molly

n_atoms = 100
box_size = SVector(2.0, 2.0, 2.0)u"nm"
temp = 298.0u"K"
atom_mass = 10.0u"u"

atoms = [Atom(mass=atom_mass, σ=0.3u"nm", ϵ=0.2u"kJ * mol^-1") for i in 1:n_atoms]
coords = place_atoms(n_atoms, box_size, 0.3u"nm")
velocities = [velocity(atom_mass, temp) for i in 1:n_atoms]
pairwise_inters = (LennardJones(),)
simulator = VelocityVerlet(dt=0.002u"ps", coupling=AndersenThermostat(temp, 1.0u"ps"))

sys = System(
    atoms=atoms,
    pairwise_inters=pairwise_inters,
    coords=coords,
    velocities=velocities,
    box_size=box_size,
    loggers=Dict("temp" => TemperatureLogger(100)),
)

simulate!(sys, simulator, 10_000)

Simulation of a protein:

using Molly

sys = System(
    joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmx_coords.gro"),
    joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmx_top_ff.top");
    loggers=Dict(
        "temp"   => TemperatureLogger(10),
        "writer" => StructureWriter(10, "traj_5XER_1ps.pdb"),
    ),
)

temp = 298.0u"K"
random_velocities!(sys, temp)
simulator = VelocityVerlet(dt=0.0002u"ps", coupling=AndersenThermostat(temp, 1.0u"ps"))

simulate!(sys, simulator, 5_000)

The above 1 ps simulation looks something like this when you view it in VMD:

Contributing

Contributions are very welcome - see the roadmap issue for more.