ruibin-liu / molly.jl Goto Github PK

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.

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, Buckingham potential, soft core variants.
• Bonded interactions - harmonic and Morse bonds, bond angles, torsion angles, harmonic position restraints, FENE bonds.
• 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 experimental support for Gromacs files.
• Verlet, velocity Verlet, Störmer-Verlet, flexible Langevin and Nosé-Hoover integrators.
• Andersen, Berendsen and velocity rescaling thermostats.
• Monte Carlo barostat and variants.
• Steepest descent energy minimization.
• Replica exchange molecular dynamics.
• Monte Carlo simulation.
• Periodic, triclinic and infinite boundary conditions.
• Constraints with SHAKE and RATTLE
• 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 the use of CellListMap.jl.
• Implicit solvent GBSA methods.
• Unitful.jl compatibility so numbers have physical meaning.
• Set up crystal systems using SimpleCrystals.jl.
• Automatic multithreading.
• GPU acceleration on CUDA-enabled devices.
• Run with Float64, Float32 or other float types.
• Some analysis functions, e.g. RDF.
• Visualise simulations as animations with Makie.jl.
• Compatibility with AtomsBase.jl and AtomsCalculators.jl.
• Differentiable molecular simulation. This is a unique feature of the package and the focus of its current development.

Features not yet implemented include:

• High GPU performance.
• Ewald or particle mesh Ewald summation.
• Full support for constrained bonds and angles.
• Protein preparation - solvent box, add hydrogens etc.
• Simulators such as metadynamics.
• Quantum mechanical modelling.
• Domain decomposition algorithms.
• Alchemical free energy calculations.
• High test coverage.
• API stability.

Julia is required, with Julia v1.7 or later required to get the latest version of Molly. It is recommended to run on the current stable Julia release for the best performance. Install Molly from the Julia REPL. Enter the package mode by pressing ] and run add Molly.

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")
temp = 298.0u"K"
atom_mass = 10.0u"g/mol"

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 = [random_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,
    coords=coords,
    boundary=boundary,
    velocities=velocities,
    pairwise_inters=pairwise_inters,
    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:

Contributions are very welcome including reporting bugs, fixing bugs, adding new features, improving performance, adding tests and improving documentation. Feel free to open an issue or use the channels below to discuss your contribution. New features will generally require tests to be added as well. See the roadmap issue for some discussion of recent progress and future plans.

Join the #juliamolsim channel on the Julia Slack, the #molly channel on the JuliaMolSim Zulip or post on the Julia Discourse to discuss the usage and development of Molly.jl.

Molly.jl follows the Contributor Covenant code of conduct.

If you use Molly, please cite the following paper (bib entry here):

• Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, Chemical Science 15, 4897-4909 (2024)

A paper involving more contributors with further details on the software will be written at some point.

There is the possibility of a postdoc position involving the development and use of Molly. Contact Joe Greener with informal enquiries.