Molly - v0.22.3

Bug fixes

• A bug when calculating the potential energy of a system using Measurements.jl is fixed.

- Julia
Published by jgreener64 11 months ago

Molly - v0.22.2

New features

• write_structure is added to allow a system to be written to a file.
• TrajectoryWriter now writes out better PDB files. StructureWriter is now an alias for TrajectoryWriter with the PDB format and will be removed in a future breaking release. It is recommended to replace instances of StructureWriter with TrajectoryWriter.
• The excluded_res and write_boundary keyword arguments can now be given to TrajectoryWriter. The atom_inds keyword argument can now be given to StructureWriter.
• AtomDatacan now store chain_id and hetero_atom, allowing better file writing.
• The Urey-Bradley potential is added as UreyBradley.
• The mixing functions waldman_hagler_σ_mixing, waldman_hagler_ϵ_mixing and fender_halsey_ϵ_mixing are added.
• Additional keyword arguments can now be provided to the System constructor taking in an AtomsBase system.

Bug fixes

• A bug when initialising forces in LangevinSplitting is fixed.
• A bug when converting from an AtomsBase system without velocities is fixed.
• A bug when setting up a system with infinite boundaries from a file is fixed.

- Julia
Published by jgreener64 11 months ago

Molly - v0.22.1

New features

• Writing out trajectory files in formats supported by Chemfiles.jl, including DCD and XTC, is added via the TrajectoryWriter logger.
• MolecularTopology can now optionally contain a list of indices of bonded atom pairs.
• The weight_special option is added to Mie.
• Functions required to calculate gradients for MorseBond are added.

Performance improvements

• Simulation with ASECalculator is made faster.

Bug fixes

• A memory issue when simulating with ASECalculator is fixed.
• A bug in nested multithreading for DistanceNeighborFinder and TreeNeighborFinder is fixed.

- Julia
Published by jgreener64 about 1 year ago

Molly - v0.22.0

The package is rewritten to use Enzyme.jl rather than Zygote.jl for differentiable simulations. This allows mutating code to be used, leading to better performance on CPU and GPU. In addition, faster CUDA kernels are added and support for other GPU backends is added via KernelAbstractions.jl.

Breaking changes

• CoordinateLogger, VelocityLogger and ForceLogger are renamed to CoordinatesLogger, VelocitiesLogger and ForcesLogger respectively for consistency.
• During system setup the gpu keyword argument is replaced by array_type, with CuArray giving the same behaviour as before. Use of other array types such as ROCArray is supported. The use_cell_list keyword argument is replaced with neighbor_finder_type, with the default depending on the backend.
• The second type parameter to System is changed from a Bool indicating whether the system is on the GPU to the array type of the system.
• Giving the force_units and energy_units is no longer required when constructing pairwise interactions such as LennardJones. In addition, mixing functions and shortcut functions can now be given to determine how to combine atomic parameters and when to skip the interaction respectively.
• The arguments to force and potential_energy for pairwise and specific interactions are changed to allow more flexible interaction definitions, depending for example on the velocities or step number.
• Differentiable simulations are no longer compatible with Zygote.jl, but can now be carried out using Enzyme.jl. This is faster and more memory-efficient.
• The solute field to Atom is removed and the atom_type field is added. weight_solute_solvent is no longer an option for LennardJones, though similar functionality is available with atom_type and mixing functions.
• box_volume is renamed to volume.
• run_loggers! is renamed to apply_loggers! to avoid confusion with the run_loggers function argument.
• The abstract types PairwiseInteraction and SpecificInteraction are removed. Custom interactions no longer need to sub-type anything.
• Extensions are added for code requiring Enzyme.jl, CUDA.jl and KernelDensity.jl, so relevant imports are now required before using those features.

Non-breaking changes

• Support for Julia versions before 1.10 is dropped.

New features

• Backends supported by KernelAbstractions.jl can be used to run simulations by using the appropriate array type or the array_type keyword argument during system setup.
• The Berendsen pressure coupling method is added as BerendsenBarostat.
• The density and dipole_moment functions are added.
• The AshbaughHatch and Yukawa potentials are added.
• VolumeLogger and DensityLogger are added.
• The rng keyword argument is added to place_atoms, place_diatomics and random_coord, allowing reproducible coordinate generation.
• The array_type function is added, giving the array type of a system or array.
• The step number can be given as a third argument with a default of 0 to forces, potential_energy and virial acting on a system. This allows time-dependent forces, with the caveat that the step number resets to 1 every time simulate! is called and can also be 0 to calculate forces before the first step.
• A method is added to random_velocities! which takes in and modifies the velocities as the first argument.

Performance improvements

• Better CUDA force and potential energy kernels significantly improve performance on CUDA compatible devices. The GPUNeighborFinder is added for this path but does not calculate neighbors, which are calculated each step in the kernels.
• Simulations are faster on both CPU and GPU due to mutating code leading to fewer memory allocations.
• System setup from a file is made much faster.
• The package is faster to load as a number of dependencies have been removed.
• The performance of implicit solvent on CPU is improved.

Bug fixes

• A bug when using more than two interactions on the GPU is fixed.
• A type conversion bug in CellListMapNeighborFinder construction is fixed.

- Julia
Published by jgreener64 over 1 year ago

Molly - v0.21.2

Non-breaking changes

• Updates are made for AtomsBase.jl 0.4. AtomsBase is no longer re-exported.

- Julia
Published by jgreener64 over 1 year ago

Molly - v0.21.1

Non-breaking changes

• Compatibility bounds are updated for various packages.

Bug fixes

• A bug in boundary gradient calculation is fixed.

- Julia
Published by jgreener64 almost 2 years ago

Molly - v0.21.0

Breaking changes

• Observable functions for GeneralObservableLogger now need to accept arbitrary keyword arguments, for example by adding kwargs... to the function call. This allows the logging changes described below.

Non-breaking changes

• Support for Julia versions before 1.9 is dropped. A package extension, rather than Requires.jl, is used to provide visualize when GLMakie.jl is imported.

New features

• ASECalculator is added, allowing Python ASE calculators to be used in Molly. The code is in a package extension available when PythonCall.jl is imported. It is the user's responsibility to have the required Python packages installed. Examples of using MACE and psi4 are given.
• current_forces and current_potential_energy can be used in logging functions to reuse properties calculated in the simulation step. They default to nothing when the properties are not available.
• Interaction types are allowed to be different for each replica in a ReplicaSystem.

Performance improvements

• PotentialEnergyLogger, TotalEnergyLogger and ForceLogger avoid recomputation when the relevant properties are calculated in the simulation step.

Bug fixes

• MollyCalculator now works in two dimensions and for other floating point types.

- Julia
Published by jgreener64 about 2 years ago

Molly - v0.20.0

Breaking changes

• apply_constraints! and SHAKE are removed as part of the changes to constraints.
• The System constructor for AtomsBase.jl systems is changed to take force_units and energy_units as keyword arguments rather than positional arguments. The defaults are consistent with the rest of Molly.
• velocity_autocorr is removed since AutoCorrelationLogger provides a more general version of this functionality.

New features

• Support for constraints is improved and documented with SHAKE_RATTLE allowing the SHAKE and RATTLE algorithms to be applied as appropriate to most simulators. DistanceConstraint, disable_constrained_interactions!, apply_position_constraints!, apply_velocity_constraints!, check_position_constraints and check_velocity_constraints are all added. Constraints are not currently compatible with GPU simulation.
• Gradients with respect to the boundary can now be calculated in some contexts.

Community

• A logo is added to the project.

Bug fixes

• A bug in FENEBond potential energy calculation is fixed.

- Julia
Published by jgreener64 about 2 years ago

Molly - v0.19.0

Breaking changes

• General interactions are changed to use the AtomsCalculators.jl interface, allowing simulations to be run with calculators from other packages. A tuple of interactions compatible with the AtomsCalculators.jl interface should be given to general_inters when constructing a System. ImplicitSolventOBC, ImplicitSolventGBN2 and MullerBrown are changed to be calculators.
• The type parameters of System and ReplicaSystem are changed.

New features

• forces, accelerations, potential_energy, total_energy, virial and pressure now calculate the neighbors by default when called without neighbors. If they are being reused, neighbors should be pre-computed as before for performance.
• System and ReplicaSystem now have a data field, set with the data keyword argument to the constructors, that can be used to store arbitrary data. This data can be accessed inside simulators.
• LennardJonesSoftCore, CoulombSoftCore and custom atom types are now compatible with gradients.

- Julia
Published by jgreener64 over 2 years ago

Molly - v0.18.4

Bug fixes

• A bug that prevented system setup on Julia 1.7 is fixed.
• A type preservation bug in the rdf function is fixed.

- Julia
Published by jgreener64 over 2 years ago

Molly - v0.18.3

New features

• Compatibility with AtomsCalculators.jl is added via MollyCalculator.
• The documentation on setting up systems from structure files is improved.
• A list of relevant publications is added to the documentation.

Community

• The Contributor Covenant Code of Conduct is added to the project.

Bug fixes

• A bug in the NoseHoover simulator when not using units is fixed.

- Julia
Published by jgreener64 over 2 years ago

Molly - v0.18.2

Performance improvements

• The vector function for calculating the displacement between coordinates accounting for periodic boundary conditions is made faster, improving simulation performance on CPU and GPU.

- Julia
Published by jgreener64 over 2 years ago

Molly - v0.18.1

New features

• Simulation of overdamped Langevin dynamics is added as OverdampedLangevin.

Performance improvements

• The performance of force calculation without a neighbor list on the GPU is significantly improved.

Bug fixes

• A bug in compatibility with SimpleCrystals.jl is fixed.

- Julia
Published by jgreener64 over 2 years ago

Molly - v0.18.0

Breaking changes

• Molar units are made more consistent throughout the package. If force and energy units are molar then the atomic masses should have a molar dimension, e.g. u"g/mol" rather than u"u". The default Boltzmann constant k is chosen based on the energy_units given to a System.

New features

• A constructor for System is added to convert from an AtomsBase.jl AbstractSystem.
• During System setup, checks are made for a consistent unit system and appropriate errors are thrown.
• Calculation of the hydrodynamic radius is added as hydrodynamic_radius.
• The charges function is added to give the partial charges of the atoms in a system.

Bug fixes

• Issues with AtomsBase.jl integration are fixed.

- Julia
Published by jgreener64 almost 3 years ago

Molly - v0.17.0

Breaking changes

• run_loggers is no longer available as a keyword argument to SteepestDescentMinimizer and log_states is no longer available as a keyword argument when calling simulate! with MetropolisMonteCarlo. Instead run_loggers can be given as a keyword argument to simulate! as described below.

New features

• The Monte Carlo anisotropic barostat is added as MonteCarloAnisotropicBarostat, allowing separate pressure coupling in each dimension.
• The Monte Carlo membrane barostat is added as MonteCarloMembraneBarostat, allowing pressure coupling for systems involving a membrane.
• A System constructor is added to create systems from a SimpleCrystals.jl Crystal struct.
• A convenience constructor is added for System allowing an existing System to be copied with given properties changed.
• run_loggers can be given as a keyword argument to simulate! to determine whether the loggers are run. The options are true, false or :skipzero, in which case the loggers are not run before the first step. run_loggers is true by default except for SteepestDescentMinimizer, where it is false. run_loggers! now has a fourth argument which determines whether the loggers are run, default true.
• The scale factor given to scale_coords! can now be a SVector corresponding to the scaling factor for each axis in addition to a single number.
• General interactions can now implement a method for virial.

Bug fixes

• A bug in force calculation with more than two interactions on the GPU is fixed.
• A bug allowing multiple 1-4 scaling values to be read from an OpenMM force field XML file is fixed.

- Julia
Published by jgreener64 almost 3 years ago

Molly - v0.16.0

Breaking changes

• apply_coupling! now returns whether the coupling has invalidated the currently stored forces, for example by changing the coordinates.
• find_neighbors now takes another optional argument which determines whether the neighbor list should be forced to recompute, regardless of the step number.
• The type parameters of System, ReplicaSystem, AtomType and Langevin are changed.

New features

• The Monte Carlo barostat is added as MonteCarloBarostat, allowing pressure coupling during simulations.
• The virial and pressure can be calculated for systems where only the pairwise interactions contribute to the virial using virial and pressure. Corresponding loggers are added as VirialLogger and PressureLogger.
• The scale_boundary, scale_coords! and molecule_centers functions are added.
• The topology keyword argument for System can provide information about which atoms are in the same molecule, with this information stored as a MolecularTopology when reading a System from a file. The corresponding keyword arguments topology and replica_topology are added to ReplicaSystem.
• Multiple couplers can be given to the coupling argument of compatible simulators as a Tuple or a NamedTuple. Langevin is now compatible with couplers.
• Warnings are given for skipped incompatible fields when reading OpenMM XML force field files. Using atom charges from residue templates is no longer required.
• The use_cell_list keyword argument is added to the System constructor from files.
• Unitful.ustrip is now defined for CubicBoundary and RectangularBoundary.

- Julia
Published by jgreener64 about 3 years ago

Molly - v0.15.0

The core of the package is rewritten to use CUDA.jl kernels on the GPU path for increased performance and GPU memory usage. Enzyme.jl is used along with Zygote.jl to differentiate through simulations on CPU and GPU for increased performance.

Breaking changes

• The nl_only field of pairwise interactions is replaced with a use_neighbors function, which accesses a use_neighbors field of the struct for built-in interactions. Custom pairwise interactions can define a method for this function, which returns false by default.
• The weight_14 field of pairwise interactions has been renamed to weight_special and the weight_14 argument to force has been renamed to special. The nb_matrix and matrix_14 fields of neighbor finders have been renamed to eligible and special respectively.
• OpenMMForceField, OpenMMResidueType and OpenMMAtomType are renamed to MolecularForceField, ResidueType and AtomType respectively.
• The penultimate argument to InteractionList1Atoms etc., the interaction type names, is now an optional final argument that defaults to a vector of empty strings. The type parameters are also changed.
• velocity is renamed to random_velocity and rand_coord is renamed to random_coord.
• DistanceVecNeighborFinder and NeighborListVec are removed since DistanceNeighborFinder and NeighborList now work on the GPU and with automatic differentiation.
• The gpu_diff_safe argument is no longer available when setting up a System since the CPU path is now differentiable. is_gpu_diff_safe is removed.
• The type parameters of System, ReplicaSystem, DistanceNeighborFinder and NeighborList are changed.
• The @fastmath macro is no longer used in the package.

Non-breaking changes

• DistanceNeighborFinder and TreeNeighborFinder now return lists of neighboring pairs in ascending order of index.

New features

• The Nosé-Hoover simulator is added as NoseHoover.
• potential_energy and total_energy are now compatible with automatic differentiation on CPU and GPU. They can also now be run in parallel using the n_threads keyword argument, with this being the default behaviour.
• CubicBoundary and RectangularBoundary can take a single value as an argument, indicating the same size in all dimensions. They must take positive side lengths.
• The remove_CM_motion argument to simulators can be set to an integer, in which case the center of mass motion is removed every given number of steps. The default remains to remove the center of mass motion every step.
• The kappa and rename_terminal_res keyword arguments are available as arguments when constructing a System from a file and a force field.
• Differentiable simulation now works with any combination of built-in or custom interactions.
• Differentiable simulation now works with multithreading on the CPU.
• The number of GPU threads used for the CUDA.jl kernels can be tuned with the environmental variables MOLLY_GPUNTHREADS_PAIRWISE, MOLLY_GPUNTHREADS_SPECIFIC, MOLLY_GPUNTHREADS_DISTANCENF and MOLLY_GPUNTHREADS_IMPLICIT.
• A section on development is added to the documentation and other areas of the documentation are expanded.

Performance improvements

• Force calculation, energy calculation, simulation and implicit solvent force/energy calculation are all made faster on CPU and GPU.
• GPU memory usage is reduced significantly, allowing the simulation of larger systems.
• Differentiable simulation is made faster on CPU and GPU.

Bug fixes

• Bugs in boundary and system indexing are fixed.
• A bug in implicit solvent automatic differentiation is fixed.
• A bug allowing incorrect units to be used in general interactions is fixed.

- Julia
Published by jgreener64 about 3 years ago

Molly - v0.14.3

Bug fixes

• A bug introduced by a new version of ForwardDiff.jl is fixed.

- Julia
Published by jgreener64 about 3 years ago

Molly - v0.14.2

New features

• The Müller-Brown potential is added as MullerBrown.

- Julia
Published by jgreener64 over 3 years ago

Molly - v0.14.1

New features

• The Buckingham potential is added as Buckingham.
• Polymer melt and density functional theory examples are added to the documentation.

Bug fixes

• A bug introduced by a new version of AtomsBase.jl is fixed. In addition, atoms in systems without atoms_data defined now return :unknown from AtomsBase.atomic_symbol.
• A bug in the export of OpenMMResidueType is fixed.

- Julia
Published by jgreener64 over 3 years ago

Molly - v0.14.0

Breaking changes

• The type parameters and fields of System, ReplicaSystem, ImplicitSolventOBC and ImplicitSolventGBN2 are changed.
• The type parameters of TemperatureREMD are changed.

Non-breaking changes

• The mass function falls back to accessing the mass field, making it easier to define custom atom types.

New features

• A Monte Carlo simulator that uses the Metropolis algorithm is added as MetropolisMonteCarlo. MonteCarloLogger is added to record acceptance information. random_uniform_translation! and random_normal_translation! are added to generate trial moves.
• HamiltonianREMD is added to allow REMD with different interactions for each replica. remd_exchange! and simulate_remd! are added to allow custom REMD simulators to be defined by giving the exchange function. replica_pairwise_inters, replica_specific_inter_lists and replica_general_inters can now be given when constructing a ReplicaSystem to allow different interactions for each replica.
• Soft core versions of the Lennard-Jones and Coulomb interactions are added as LennardJonesSoftCore and CoulombSoftCore.
• Preliminary support for bonded constraints using the SHAKE algorithm is added via SHAKE and apply_constraints!. constraints can be used to define the constraints when constructing a System, with corresponding arguments for a ReplicaSystem. This feature is still under development and is not fully documented yet.
• Additional keyword arguments can now be used in log_property!, making the logging of properties in custom simulators easier.
• A section on related software is added to the documentation.

Performance improvements

• Implicit solvent force and energy calculation are made faster and more memory efficient.

Bug fixes

• A bug when constructing the Mie potential with certain parameters is fixed.

- Julia
Published by jgreener64 over 3 years ago

Molly - v0.13.0

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.

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.12.1

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

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.12.0

• 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.

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.11.0

• 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.

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.10.4

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

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.10.3

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

- Julia
Published by jgreener64 almost 4 years ago

Molly - v0.10.2

• 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.

- Julia
Published by jgreener64 about 4 years ago

Molly - v0.10.1

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

- Julia
Published by jgreener64 about 4 years ago

Molly - v0.10.0

• 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.

- Julia
Published by jgreener64 about 4 years ago

Molly - v0.9.0

• 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.

- Julia
Published by jgreener64 about 4 years ago

Molly - v0.8.0

• 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.

- Julia
Published by jgreener64 over 4 years ago

Molly - v0.7.0

• 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.

- Julia
Published by jgreener64 over 4 years ago

Molly - v0.6.0

• 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.

- Julia
Published by jgreener64 over 4 years ago

Molly - v0.5.0

• 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.

- Julia
Published by jgreener64 over 4 years ago

Molly - v0.4.0

• 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.

- Julia
Published by jgreener64 over 4 years ago

Molly - v0.3.0

• 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.

- Julia
Published by jgreener64 about 5 years ago

Molly - v0.2.2

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

- Julia
Published by jgreener64 over 5 years ago

Molly - v0.2.1

• 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.

- Julia
Published by jgreener64 over 5 years ago

Molly - v0.2.0

• 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.

- Julia
Published by jgreener64 over 5 years ago

Molly - v0.1.0

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.

- Julia
Published by jgreener64 almost 6 years ago