NEWS.md

Molly.jl release notes

v0.13.0 - Aug 2022

Breaking changes

• The minimum distance argument to place_atoms and place_diatomics is now the keyword argument min_dist with a default value of no distance. place_diatomics now places the molecules facing random directions, with the old behaviour available by setting aligned=true. place_diatomics now checks for sensible inputs and terminates after a certain number of failed attempts like place_atoms.
• The argument order in apply_coupling! is switched from apply_coupling!(system, simulator, coupling) to apply_coupling!(system, coupling, simulator).
• The default mass of an Atom is changed from 0.0u"u" to 1.0u"u".
• The AbstractNeighborFinder abstract type is removed.
• The centre_coords keyword argument when constructing a System from files is renamed to center_coords.
• Center of mass motion is now removed before loggers are run at step zero of a simulation, matching the behaviour during the simulation steps.

Non-breaking changes

• visualize shows the boundary as lines by default and has the show_boundary, boundary_linewidth and boundary_color keyword arguments added.

New features

• Temperature replica exchange MD (REMD) can now be run in parallel. The ReplicaSystem struct is added to act as a container for multiple Systems. The TemperatureREMD simulator and ReplicaExchangeLogger are added to set up and run replica exchange simulations.
• TriclinicBoundary is added and can be used to simulate periodic boundary conditions in a triclinic box. A TriclinicBoundary can be constructed from either 3 basis vectors or 3 basis vector lengths and angles α/β/γ. The box_center function is added.

Bug fixes

• Coordinates are now moved back inside the boundary before the first step of the simulation.

v0.12.1 - Aug 2022

• Updates are made to support the latest Zygote.jl and UnitfulChainRules.jl versions.
• A bug in implicit solvent gradient setup is fixed.

v0.12.0 - Jul 2022

• The parallel keyword argument is renamed to n_threads throughout, allowing an exact number of threads to be specified with the default remaining Threads.nthreads().
• Arguments for bonded interactions are made more consistent: HarmonicBond has kb renamed to k and b0 to r0, HarmonicAngle has cth renamed to k and th0 to θ0, and MorseBond has α renamed to a.
• An additional type parameter is added to System that records whether it is on the GPU. The is_on_gpu function is added to access this property.
• The Interaction abstract type is removed.
• The HarmonicPositionRestraint interaction for restraining atomic positions, commonly used during equilibration of biomolecular systems, is added. InteractionList1Atoms and SpecificForce1Atoms are added to allow the definition of interactions that apply a force to one atom. The add_position_restraints function is added to apply position restraints to a System, along with the atom selector functions is_any_atom and is_heavy_atom.
• The CosineAngle interaction for the cosine bond angle between three atoms is added.
• The FENEBond interaction for the finitely extensible non-linear elastic (FENE) bond between two atoms is added.
• The masses function to access the mass of each atom in a System is added.
• AndersenThermostat is made differentiable.
• DistanceNeighborFinder and TreeNeighborFinder now use FLoops.jl and show improved performance on multiple threads.
• Inconsistent System setup now throws an error.
• Equations are added to some docstrings.

v0.11.0 - Jun 2022

• box_size is renamed to boundary throughout. Boundaries of the form SVector(1.0, 2.0, 3.0) should be replaced by CubicBoundary(1.0, 2.0, 3.0), allowing non-cubic boundaries to be added in future. Setting one or more values to Inf gives no boundary in that dimension. RectangularBoundary should be used for 2D simulations. float_type, box_volume and AtomsBase.n_dimensions are defined for boundaries.
• The recorded values in loggers are now accessed with Base.values. Loggers are now given to the System as a named tuple rather than as a Dict for performance reasons.
• wrap_coords_vec is renamed to wrap_coords, wrap_coords is renamed to wrap_coord_1D, vector1D is renamed to vector_1D, the cutoff argument to the implicit solvent models is renamed to dist_cutoff, and the nl_dist argument to System is renamed to dist_neighbors.
• The general LangevinSplitting simulator is added to allow a variety of integrators to be defined such as velocity Verlet (splitting "BAB"), the Langevin implementation in Langevin ("BAOA"), and symplectic Euler integrators ("AB" and "BA").
• GeneralObservableLogger is added to periodically record a given observable throughout the simulation. Most existing loggers are changed to be cases of GeneralObservableLogger. AverageObservableLogger is also added and records a running average rather than storing observations.
• TimeCorrelationLogger is added to calculate correlations between observables. AutoCorrelationLogger corresponds to the case when the two observables are the same.
• The keyword argument k to System, velocity and maxwell_boltzmann allows a custom Boltzmann constant to be used.
• More of the package is made differentiable due to the use of UnitfulChainRules.jl.

v0.10.4 - Jun 2022

• Visualisation is updated to use GLMakie.jl v0.6.

v0.10.3 - Jun 2022

• place_atoms now checks for sensible inputs and terminates after a certain number of failed attempts.
• A bug in precompilation is fixed.

v0.10.2 - May 2022

• ForceLogger is added.
• The parallel keyword argument is now available in the log_property! function.
• More examples are added to the documentation.
• A bug in the Mie potential energy is fixed.

v0.10.1 - May 2022

• A bug in the Gravity force and potential energy is fixed.

v0.10.0 - Apr 2022

• Loggers now also run before the first simulation step, i.e. at step 0, allowing the starting state to be recorded.
• inject_gradients now returns general interactions in addition to atoms, pairwise interactions and specific interaction lists.
• Steepest descent energy minimization is added via SteepestDescentMinimizer.
• GPU support is added for potential_energy.
• The radius_gyration function is added.
• A kappa value for ionic screening may be given to ImplicitSolventOBC and ImplicitSolventGBN2.
• Improvements are made to simulation setup such as allowing multiple macromolecular chains.
• A random number generator can now be passed to Langevin, allowing reproducible simulations.
• Gradients through the GB-Neck2 interaction are made to work on the GPU.
• Bugs in StormerVerlet are fixed.
• The possibility of a NaN value for the HarmonicAngle force when the angle is π is fixed.
• A bug causing random_velocities to run slowly is fixed.

v0.9.0 - Mar 2022

• The arguments to forces and accelerations are made consistent across implementations.
• Centre of mass motion is removed by default during simulation using remove_CM_motion!.
• Coordinates are centred in the simulation box by default during setup.
• The Langevin integrator and Verlet integrator are added.
• The MorseBond potential is added.
• The GB-Neck2 implicit solvent model is added via ImplicitSolventGBN2.
• The CubicSplineCutoff is added.
• The rmsd function is added.
• The AtomsBase.jl interface is made more complete.
• The progress bar is removed from simulations.
• The out-of-place neighbor list type NeighborListVec is changed.

v0.8.0 - Feb 2022

• General interactions are renamed to pairwise interactions throughout to better reflect their nature. The abstract type is now PairwiseInteraction and the keyword argument to System is now pairwise_inters. General interaction now refers to a new type of interaction that takes in the whole system and returns forces for all atoms, allowing interactions such as neural network potentials acting on the whole system. This is available via the keyword argument general_inters to System.
• Implicit solvent models are added via the ImplicitSolventOBC general interaction type and the implicit_solvent keyword argument when setting up a System from a file. The Onufriev-Bashford-Case GBSA model with parameter sets I and II is provided.
• charge is added to access the partial charge of an Atom.
• The box_size keyword argument may be given when setting up a System from a file.
• A bug in KineticEnergyLogger is fixed.

v0.7.0 - Jan 2022

• The force and potential_energy functions for general interactions now take the vector between atom i and atom j as an argument in order to save on computation.
• Differentiable simulations are made faster and more memory-efficient.
• The AtomsBase.jl interface is updated to v0.2 of AtomsBase.jl.
• extract_parameters and inject_gradients are added to assist in taking gradients through simulations.
• bond_angle and torsion_angle are added.
• random_velocities is added.
• A solute field is added to Atom allowing solute-solvent weighting in interactions. This is added to the LennardJones interaction.
• A proper field is added to PeriodicTorsion.
• The float type is added as a type parameter to System. float_type and is_gpu_diff_safe are added to access the type parameters of a System.
• A types field is added to types such as InteractionList2Atoms to record interaction types.
• find_neighbors can now be given just the system as an argument.
• Visualisation is updated to use GLMakie.jl v0.5.
• Bugs in velocity generation and temperature calculation with no units are fixed.

v0.6.0 - Jan 2022

• Differentiable simulation works with Zygote reverse and forward mode AD on both CPU and GPU. General and specific interactions are supported along with neighbor lists. It does not currently work with units, user-defined types and some components of the package.
• Significant API changes are made including a number of functions being renamed, thermostats being renamed to couplers and the removal of some types.
• Simulation is renamed to System and the time step and coupling are passed to the simulator, which is passed to the simulate! function.
• System is a sub-type of AbstractSystem from AtomsBase.jl and the relevant interface is implemented, allowing interoperability with the wider ecosystem.
• Specific interactions are changed to store indices and parameters as part of types such as InteractionList2Atoms. Specific interaction force functions now return types such as SpecificForce4Atoms. Specific interactions can now run on the GPU.
• Some abstract types are removed. NeighborFinder is renamed to AbstractNeighborFinder.
• The potential_energy function arguments match the force function arguments.
• File reader setup functions are called using System and return a System directly.
• find_neighbors! is renamed to find_neighbors and returns the neighbors, which are no longer stored as part of the simulation.
• VelocityFreeVerlet is renamed to StormerVerlet.
• RescaleThermostat and BerendsenThermostat are added.
• random_velocities! and velocity_autocorr are added.
• VelocityLogger, KineticEnergyLogger and PotentialEnergyLogger are added.
• DistanceVecNeighborFinder is added for use on the GPU.
• Atomic charges are now dimensionless, i.e 1.0 is an atomic charge of +1.
• HarmonicAngle now works in 2D.
• Support for Julia versions before 1.7 is dropped.

v0.5.0 - Oct 2021

• Readers are added for OpenMM XML force field files and coordinate files supported by Chemfiles.jl. Forces, energies and the results of a short simulation exactly match the OpenMM reference implementation for a standard protein in the a99SB-ILDN force field.
• A cell neighbor list is added using CellListMap.jl.
• CoulombReactionField is added to calculate long-range electrostatic interactions.
• The PeriodicTorsion interaction is added and the previous Ryckaert-Bellemans Torsion is renamed to RBTorsion.
• Support for weighting non-bonded interactions between atoms in a 1-4 interaction is added.
• The box size is changed from one value to three, allowing a larger variety of periodic box shapes.
• Support for different mixing rules is added for the Lennard-Jones interaction, with the default being Lorentz-Bertelot mixing.
• A simple DistanceCutoff is added.
• Excluded residue names can now be defined for a StructureWriter.
• The placediatomics and ustripvec functions are added.
• The AtomMin type is removed, with Atom now being a bits type and AtomData used to store atom data.
• Visualisation now uses GLMakie.jl.
• adjust_bounds is renamed to wrapcoords.

v0.4.0 - Sep 2021

• Unitful.jl support is added and recommended for use, meaning numbers have physical meaning and many errors are caught. More type parameters have been added to various types to allow this. It is still possible to run simulations without units by specifying the force_unit and energy_unit arguments to Simulation.
• Interaction constructors with keyword arguments are added or improved.
• The maximum force for non-bonded interactions is removed.

v0.3.0 - May 2021

• The spelling of "neighbour" is changed to "neighbor" throughout the package. This affects NoNeighborFinder, DistanceNeighborFinder, TreeNeighborFinder, find_neighbors! and the neighbor_finder argument to Simulation.
• Torsion angle force calculation is improved.
• A bug in force calculation for specific interactions is fixed.
• Support for Julia versions before 1.6 is dropped.

v0.2.2 - Feb 2021

• The TreeNeighbourFinder is added for faster distance neighbour finding using NearestNeighbors.jl.

v0.2.1 - Dec 2020

• Documentation is added for cutoffs.
• Compatibility bounds are updated for various packages, including requiring CUDA.jl version 2.
• Support for Julia versions before 1.5 is dropped.

v0.2.0 - Sep 2020

• Shifted potential and shifted force cutoff approaches for non-bonded interactions are introduced.
• An EnergyLogger is added and the potential energy for existing interactions defined.
• Simulations can now be run with the CuArray type from CUDA.jl, allowing GPU acceleration.
• The in-place force! functions are changed to out-of-place force functions with different arguments.
• The i-i self-interaction is no longer computed for force functions.
• The Mie potential is added.
• The list of neighbours is now stored in the Simulation type.
• Documentation is added for experimental differentiable molecular simulation.
• Optimisations are implemented throughout the package.
• Support for Julia versions before 1.3 is dropped.

v0.1.0 - Jun 2020

Initial release of Molly.jl, a Julia package for molecular simulation.

Features:

• Interface to allow definition of new forces, simulators, thermostats, neighbour finders, loggers etc.
• Read in pre-computed Gromacs topology and coordinate files with the OPLS-AA forcefield and run MD on proteins with given parameters. In theory it can do this for any regular protein, but in practice this is untested.
• Non-bonded interactions - Lennard-Jones Van der Waals/repulsion force, electrostatic Coulomb potential, gravitational potential, soft sphere potential.
• Bonded interactions - covalent bonds, bond angles, torsion angles.
• Andersen thermostat.
• Velocity Verlet and velocity-free Verlet integration.
• Explicit solvent.
• Periodic boundary conditions in a cubic box.
• Neighbour list to speed up calculation of non-bonded forces.
• Automatic multithreading.
• Some analysis functions, e.g. RDF.
• Run with Float64 or Float32.
• Physical agent-based modelling.
• Visualise simulations as animations.