Uses of Package
ffx.potential.parameters
Packages that use ffx.potential.parameters
Package
Description
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Extended package is progress toward support for constant pH molecular dynamics using extended
system variables (i.e. lambda dynamics on protonation).
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
The implicit package implements implicit solvent models and related terms,
including Generalized Kirkwood (GK) electrostatics, surface area terms,
dispersion/cavitation contributions, and supporting parallel regions for
Born radii and field evaluation.
The pme package implements polarization and permanent electrostatics using
Particle Mesh Ewald (PME).
The openmm package contains utilities to construct and run Force Field X
potentials on the OpenMM platform, including system builders, custom forces,
alchemical fixed-charge forces, and integrators tailored to FFX simulations.
The Parameters package stores force field atom types, bond types, etc, and keywords that define
the potential.
The Parsers package handles reading/writing files to/from the internal data structure.
The terms package contains analytical potential energy terms and their
gradients for bonded interactions (bond, angle, stretch-bend, torsions,
impropers, Urey-Bradley) and restraint terms used by Force Field X.
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Classes in ffx.potential.parameters used by ffx.algorithms.optimizeClassDescriptionThe ForceField class organizes parameters for a molecular mechanics force field.
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Classes in ffx.potential.parameters used by ffx.potentialClassDescriptionAngle modes include Normal or In-PlaneThe ForceField class organizes parameters for a molecular mechanics force field.
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Classes in ffx.potential.parameters used by ffx.potential.bondedClassDescriptionThe AngleType class defines one harmonic angle bend energy term.Angle modes include Normal or In-PlaneThe AtomType class represents one molecular mechanics atom type.The BondType class defines one harmonic bond stretch energy term.The ForceField class organizes parameters for a molecular mechanics force field.The ImproperTorsionType class defines an improper torsion.The MultipoleType class defines a multipole in its local frame.The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.The PolarizeType class defines an isotropic atomic polarizability.The SoluteType class defines one implicit solvent radius.The StretchBendType class defines one out-of-plane angle bending energy type.Utilities for interpolating between Amino Acid protonation and tautomer states.The TorsionTorsionType class defines a Torsion-Torsion spline.The TorsionType class defines a torsional angle.The UreyBradleyType class defines one harmonic UreyBradley cross term.The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.
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Classes in ffx.potential.parameters used by ffx.potential.extendedClassDescriptionUtilities for interpolating between Amino Acid protonation and tautomer states.
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Classes in ffx.potential.parameters used by ffx.potential.nonbondedClassDescriptionThe ForceField class organizes parameters for a molecular mechanics force field.The MultipoleType class defines a multipole in its local frame.The PolarizeType class defines an isotropic atomic polarizability.Epsilon combining rule.Radius combining rule.Radius size in the parameter file (radius or diameter).Radius type in the parameter file (R-Min or Sigma).VDW Type.
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Classes in ffx.potential.parameters used by ffx.potential.nonbonded.implicitClassDescriptionThe ForceField class organizes parameters for a molecular mechanics force field.
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Classes in ffx.potential.parameters used by ffx.potential.nonbonded.pmeClassDescriptionThe ForceField class organizes parameters for a molecular mechanics force field.The local multipole frame is defined by the Z-then-X or Bisector convention.
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Classes in ffx.potential.parameters used by ffx.potential.openmmClassDescriptionDescribes the function used by the bond.The ForceField class organizes parameters for a molecular mechanics force field.
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Classes in ffx.potential.parameters used by ffx.potential.parametersClassDescriptionThe AngleTorsionType class defines one angle-torsion energy type.The AngleType class defines one harmonic angle bend energy term.Angle function types include harmonic or sextic.Angle modes include Normal or In-PlaneThe AtomType class represents one molecular mechanics atom type.All force field types should extend the BaseType class.The BioType class maps PDB identifiers to atom types.The BondType class defines one harmonic bond stretch energy term.Describes the function used by the bond.The ChargeType class defines a partial atomic charge type.The ForceField class organizes parameters for a molecular mechanics force field.Available force fields.The ImproperTorsionType class defines an improper torsion.The MultipoleType class defines a multipole in its local frame.The local multipole frame is defined by the Z-then-X or Bisector convention.The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.The PolarizeType class defines an isotropic atomic polarizability.A BaseType for relative solvation energies (intended for nonstandard amino acids).The SoluteType class defines one implicit solvent radius.The StretchBendType class defines one out-of-plane angle bending energy type.The StretchTorsionType class defines one stretch-torsion energy type.Constant
CysteineAtomsConstantHistidineAtomsConstantlysineAtomsAmino acid protonation reactions.The TorsionTorsionType class defines a Torsion-Torsion spline.The TorsionType class defines a torsional angle.Torsion modes include Normal or In-PlaneThe UreyBradleyType class defines one harmonic UreyBradley cross term.The VDWPairType class defines a van der Waals Pair type.The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.Epsilon combining rule.Radius combining rule.Radius size in the parameter file (radius or diameter).Radius type in the parameter file (R-Min or Sigma).VDW Type.Torsion modes include Normal or In-Plane -
Classes in ffx.potential.parameters used by ffx.potential.parsersClassDescriptionThe ForceField class organizes parameters for a molecular mechanics force field.
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Classes in ffx.potential.parameters used by ffx.potential.terms