Uses of Package
ffx.potential

Packages that use ffx.potential

Package	Description
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators	The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats	The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.anneal
ffx.algorithms.optimize.manybody
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.pme
ffx.potential.openmm
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils	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.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.realspace.cli	The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.parsers	The Parsers package reads and writes CCP4 map files.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.commands	The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli	The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.parsers	The Parsers package reads CNS files and reads/writes MTZ files.

Classes in ffx.potential used by ffx.algorithms

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.cli

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.dynamics

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
SystemState	The current state of the molecular dynamics simulation.
UnmodifiableState	A record class to hold the state of a system.

Classes in ffx.potential used by ffx.algorithms.dynamics.integrators

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
SystemState	The current state of the molecular dynamics simulation.

Classes in ffx.potential used by ffx.algorithms.dynamics.thermostats

Class	Description
SystemState	The current state of the molecular dynamics simulation.

Classes in ffx.potential used by ffx.algorithms.mc

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.misc

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.optimize

Class	Description
AssemblyState	The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
Platform	Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and OpenMM implementations (Reference, CUDA and OpenCL).
XtalEnergy	This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.

Classes in ffx.potential used by ffx.algorithms.optimize.anneal

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.optimize.manybody

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.algorithms.thermodynamics

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.potential

Class	Description
AssemblyState	The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
DualTopologyEnergy	Compute the potential energy and derivatives for a dual-topology system.
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
MolecularAssembly.FractionalMode
Platform	Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and OpenMM implementations (Reference, CUDA and OpenCL).
SystemState	The current state of the molecular dynamics simulation.
UnmodifiableState	A record class to hold the state of a system.
Utilities.FileType	An enumeration of recognized file types.
Utilities.PolymerType	An enumeration of recognized organic polymers.

Classes in ffx.potential used by ffx.potential.bonded

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.potential.cli

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.potential.commands

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.

Classes in ffx.potential used by ffx.potential.extended

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
SystemState	The current state of the molecular dynamics simulation.

Classes in ffx.potential used by ffx.potential.nonbonded

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.potential.nonbonded.pme

Class	Description
Platform	Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and OpenMM implementations (Reference, CUDA and OpenCL).

Classes in ffx.potential used by ffx.potential.openmm

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
Platform	Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and OpenMM implementations (Reference, CUDA and OpenCL).

Classes in ffx.potential used by ffx.potential.parsers

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
Utilities.FileType	An enumeration of recognized file types.

Classes in ffx.potential used by ffx.potential.utils

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.realspace

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.realspace.cli

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.realspace.parsers

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.ui

Class	Description
ForceFieldEnergy	Compute the potential energy and derivatives of a molecular system described by a force field.
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.ui.commands

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.xray

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.xray.cli

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Classes in ffx.potential used by ffx.xray.parsers

Class	Description
MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water