Uses of Interface
ffx.numerics.Potential
Packages that use Potential
Package
Description
The Algorithms package has support for local and global optimization, molecular dynamics
simulations, and calculation of free energy differences.
The Algorithms CLI package defines options for PicoCLI command line scripts.
The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and
via OpenMM.
The Integrators package implements integrators for molecular dynamics simulations.
The MC package implements a variety of Monte Carlo moves for optimization and simulation
algorithms.
The Misc package contains a few miscellaneous algorithms.
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The Thermodynamics package computes free energy differences using Orthogonal Space Tempering
(OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
The Crystal package implements space group symmetry and periodic boundary condition support.
The Numerics package has support for atomic double arrays, FFTs (1D and 3D), numerical
integration (1D), complex numbers, vector operations, multipole tensors, multi-dimensional
optimization, special functions, splines and switching functions.
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Potential CLI package defines reusable options for PicoCLI command line scripts.
The Extended package is progress toward support for constant pH molecular dynamics using extended
system variables (i.e. lambda dynamics on protonation).
The Utils package implements core functionality needed for using the Potential package, such as
opening and closing structure files, basic force field energy evaluations, etc.
The Real Space package implements real space structure refinement.
The UI package provides views and controllers for manipulating molecular systems.
The X-ray package implements support for X-ray and Neutron refinement.
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Uses of Potential in ffx.algorithms
Methods in ffx.algorithms that return PotentialModifier and TypeMethodDescriptionAlgorithmFunctions.minimize
(MolecularAssembly assembly, double eps) Relax the coordinates of a MolecularAssembly and minimize its potential energyAlgorithmUtils.minimize
(MolecularAssembly assembly, double eps) Relax the coordinates of a MolecularAssembly and minimize its potential energy -
Uses of Potential in ffx.algorithms.cli
Methods in ffx.algorithms.cli that return types with arguments of type PotentialModifier and TypeMethodDescriptionAlgorithmsScript.getPotentials()
Returns a List of all Potential objects associated with this script.Methods in ffx.algorithms.cli with parameters of type PotentialModifier and TypeMethodDescriptionAnnealOptions.createAnnealer
(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener) Creates a SimulatedAnnealing object.AnnealOptions.createAnnealer
(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile) Creates a SimulatedAnnealing object.void
MultiDynamicsOptions.distribute
(MolecularAssembly[] molecularAssemblies, Potential[] potentials, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize) If residues selected for distributing initial configurations, performs many-body optimization for this distribution.DynamicsOptions.getDynamics
(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener) Initialize a MolecularDynamics from the parsed options.DynamicsOptions.getDynamics
(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener, MDEngine requestedEngine) Initialize a MolecularDynamics from the parsed options. -
Uses of Potential in ffx.algorithms.dynamics
Classes in ffx.algorithms.dynamics that implement PotentialModifier and TypeClassDescriptionclass
The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.Methods in ffx.algorithms.dynamics that return types with arguments of type PotentialMethods in ffx.algorithms.dynamics with parameters of type PotentialModifier and TypeMethodDescriptionstatic MolecularDynamics
MolecularDynamics.dynamicsFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator) Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementationstatic MolecularDynamics
MolecularDynamics.dynamicsFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, MDEngine engine) dynamicsFactory.Constructors in ffx.algorithms.dynamics with parameters of type PotentialModifierConstructorDescriptionMolecularDynamics
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator) Constructor for MolecularDynamics.MolecularDynamicsOpenMM
(MolecularAssembly assembly, Potential potential, AlgorithmListener listener, ThermostatEnum thermostat, IntegratorEnum integrator) Constructs an MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.PhReplicaExchange
(MolecularDynamics molecularDynamics, File structureFile, double pH, double[] pHLadder, double temp, ExtendedSystem extendedSystem, double[] x, MolecularDynamicsOpenMM molecularDynamicsOpenMM, Potential potential, int worldSize) OpenMM cycled pHReplicaExchange constructor. -
Uses of Potential in ffx.algorithms.dynamics.integrators
Methods in ffx.algorithms.dynamics.integrators with parameters of type PotentialModifier and TypeMethodDescriptionvoid
Integrator pre-force evaluation operation.abstract void
Integrator pre-force evaluation operation.void
Integrator pre-force evaluation operation.void
Integrator pre-force evaluation operation.void
Integrator pre-force evaluation operation. -
Uses of Potential in ffx.algorithms.mc
Methods in ffx.algorithms.mc that return PotentialConstructors in ffx.algorithms.mc with parameters of type PotentialModifierConstructorDescriptionMDMove
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile) Constructor for MDMove.MolecularMC
(MolecularAssembly molecularAssembly, Potential potential) Constructs a DefaultMC instance with a molecular assembly and a specific Potential. -
Uses of Potential in ffx.algorithms.misc
Constructors in ffx.algorithms.misc with parameters of type PotentialModifierConstructorDescriptionGenerateRotamers
(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener) Intended to create rotamer sets for nonstandard amino acids.GenerateRotamers
(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener, RotamerLibrary library) Intended to create rotamer sets for nonstandard amino acids. -
Uses of Potential in ffx.algorithms.optimize
Fields in ffx.algorithms.optimize declared as PotentialModifier and TypeFieldDescriptionprotected final Potential
Minimize.potential
The potential energy to optimize.protected final Potential
PhMinimize.potential
The potential energy to optimize.protected final Potential
RotamerOptimization.potential
The Potential to evaluate during rotamer optimization.Methods in ffx.algorithms.optimize that return PotentialModifier and TypeMethodDescriptionCrystalMinimize.minimize
(int m, double eps, int maxIterations) minimizeMinimize.minimize()
minimizeMinimize.minimize
(double eps) minimizeMinimize.minimize
(double eps, int maxIterations) minimizeMinimize.minimize
(int m, double eps, int maxIterations) minimizeMinimizeOpenMM.minimize
(double eps, int maxIterations) minimizeMinimizeOpenMM.minimize
(int m, double eps, int maxIterations) Note the OpenMM L-BFGS minimizer does not accept the parameter "m" for the number of previous steps used to estimate the Hessian.PhMinimize.minimizeCoordinates()
minimizePhMinimize.minimizeCoordinates
(double eps) minimizePhMinimize.minimizeCoordinates
(double eps, int maxIterations) minimizePhMinimize.minimizeCoordinates
(int m, double eps, int maxIterations) minimizePhMinimize.minimizeTitration
(double eps, int maxIterations) minimizePhMinimize.minimizeTitration
(int m, double eps, int maxIterations) minimizeMethods in ffx.algorithms.optimize with parameters of type PotentialModifier and TypeMethodDescriptionstatic Minimize.MinimizationEngine
Minimize.defaultEngine
(MolecularAssembly molecularAssembly, Potential potentialEnergy) static Minimize
Minimize.minimizeFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, Minimize.MinimizationEngine engine) dynamicsFactory.Constructors in ffx.algorithms.optimize with parameters of type PotentialModifierConstructorDescriptionMinimize
(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener) Constructor for Minimize.PhMinimize
(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, ExtendedSystem esvSystem) Constructor for Minimize.RotamerOptimization
(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener) RotamerOptimization constructor. -
Uses of Potential in ffx.algorithms.optimize.anneal
Constructors in ffx.algorithms.optimize.anneal with parameters of type PotentialModifierConstructorDescriptionSimulatedAnnealing
(MolecularAssembly molecularAssembly, Potential potentialEnergy, AlgorithmListener algorithmListener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, AnnealingSchedule annealingSchedule, long mdSteps, double timeStep, boolean reInitVelocity, File dynFile) Constructor for SimulatedAnnealing. -
Uses of Potential in ffx.algorithms.optimize.manybody
Constructors in ffx.algorithms.optimize.manybody with parameters of type PotentialModifierConstructorDescriptionEnergyExpansion
(RotamerOptimization rO, DistanceMatrix dM, EliminatedRotamers eR, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, List<Residue> allResiduesList, int[][] resNeighbors, boolean threeBodyTerm, boolean decomposeOriginal, boolean usingBoxOptimization, boolean verbose, boolean pruneClashes, boolean prunePairClashes, boolean master) -
Uses of Potential in ffx.algorithms.thermodynamics
Classes in ffx.algorithms.thermodynamics that implement PotentialModifier and TypeClassDescriptionclass
An implementation of the Orthogonal Space Tempering algorithm.Methods in ffx.algorithms.thermodynamics that return PotentialModifier and TypeMethodDescriptionOrthogonalSpaceTempering.getPotentialEnergy()
getPotentialEnergy.Constructors in ffx.algorithms.thermodynamics with parameters of type PotentialModifierConstructorDescriptionMonteCarloOST
(Potential potentialEnergy, OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, AlgorithmListener listener, DynamicsOptions dynamics, boolean verbose, int cycleLength, File dynRestartFile) Constructor for MonteCarloOST. -
Uses of Potential in ffx.crystal
Subinterfaces of Potential in ffx.crystalModifier and TypeInterfaceDescriptioninterface
The CrystalPotential interface extends Potential to provide methods that change the periodic boundary conditions and symmetry via a Crystal instance. -
Uses of Potential in ffx.numerics
Methods in ffx.numerics that return types with arguments of type PotentialModifier and TypeMethodDescriptionOptimizationInterface.getUnderlyingPotentials()
Returns a List of Potentials this Potential depends on with a recursive search, excluding the top level of this call. -
Uses of Potential in ffx.potential
Classes in ffx.potential that implement PotentialModifier and TypeClassDescriptionclass
class
Compute the potential energy and derivatives for a dual-topology system.class
Compute the potential energy and derivatives of a molecular system described by a force field.class
Implements an error-canceling quad topology, where two large dual-topology simulation legs are run simultaneously to arrive at a small sum.class
This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.Methods in ffx.potential that return types with arguments of type PotentialModifier and TypeMethodDescriptionDualTopologyEnergy.getUnderlyingPotentials()
QuadTopologyEnergy.getUnderlyingPotentials()
Methods in ffx.potential with parameters of type PotentialModifier and TypeMethodDescriptionstatic double
FiniteDifferenceUtils.computedEdL
(Potential potential, LambdaInterface lambdaInterface, ForceField forceField) Compute dE/dL using finite differences. -
Uses of Potential in ffx.potential.cli
Methods in ffx.potential.cli that return PotentialModifier and TypeMethodDescriptionTopologyOptions.assemblePotential
(MolecularAssembly[] assemblies, int threadsAvail, StringBuilder sb) Performs the bulk of the work of setting up a multi-topology system.TopologyOptions.getTopology
(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb) Configure a Dual-, Quad- or Oct- Topology.Methods in ffx.potential.cli that return types with arguments of type PotentialModifier and TypeMethodDescriptionPotentialCommand.getPotentials()
Returns a List of all Potential objects associated with this script.PotentialScript.getPotentials()
Returns a List of all Potential objects associated with this script. -
Uses of Potential in ffx.potential.commands
Methods in ffx.potential.commands that return types with arguments of type Potential -
Uses of Potential in ffx.potential.extended
Classes in ffx.potential.extended that implement Potential -
Uses of Potential in ffx.potential.openmm
Classes in ffx.potential.openmm that implement PotentialModifier and TypeClassDescriptionclass
Compute the potential energy and derivatives using OpenMM. -
Uses of Potential in ffx.potential.utils
Constructors in ffx.potential.utils with parameters of type Potential -
Uses of Potential in ffx.realspace
Classes in ffx.realspace that implement PotentialModifier and TypeClassDescriptionclass
Combine the Real Space target and chemical potential energy. -
Uses of Potential in ffx.ui
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Uses of Potential in ffx.xray
Modifier and TypeClassDescriptionclass
Combine the X-ray target and chemical potential energy using theCrystalPotential
interfaceclass
Combine the X-ray target and chemical potential energy.