CoryKornowicz / Molly.jl

Molecular simulation in Julia

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. The package is described in a talk at the JuliaMolSim minisymposium at JuliaCon 2022.

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 - harmonic and Morse bonds, bond angles, torsion angles, harmonic position restraints.
• 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.
• Verlet, velocity Verlet, Störmer-Verlet and flexible Langevin integrators.
• Steepest descent energy minimization.
• Replica exchange molecular dynamics.
• Periodic, triclinic and infinite boundary conditions in a cubic box.
• Flexible loggers to track arbitrary properties throughout simulations.
• Cutoff algorithms for non-bonded interactions.
• Various neighbor list implementations to speed up the calculation of non-bonded forces, including use of CellListMap.jl.
• Implicit solvent GBSA methods.
• 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 with Makie.jl.
• 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 metadynamics.
• Other temperature or pressure coupling methods.
• Particle mesh Ewald summation.
• Protein preparation - solvent box, add hydrogens etc.
• Quantum mechanical modelling.
• Constrained bonds and angles.
• Domain decomposition algorithms.
• Alchemical free energy calculations.
• High test coverage.
• API stability.
• High GPU performance.

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
boundary = CubicBoundary(2.0u"nm", 2.0u"nm", 2.0u"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, boundary; min_dist=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,
    boundary=boundary,
    loggers=(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=(
        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.

Join the #molly channel on the JuliaMolSim Zulip to discuss the usage and development of Molly.jl.