Uses of Package
ffx.potential.nonbonded
Packages that use ffx.potential.nonbonded
Package
Description
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
The X-ray package implements support for X-ray and Neutron refinement.
-
Classes in ffx.potential.nonbonded used by ffx.potentialClassDescriptionThis Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a
NeighborList.This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using aNeighborListfor anyCrystalspace group.Apply a restraint between groups.Restrain the position of atoms to their initial coordinates.The Van der Waals class computes Van der Waals interaction in parallel using aNeighborListfor anyCrystal. -
Classes in ffx.potential.nonbonded used by ffx.potential.nonbondedClassDescriptionThis Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a
NeighborList.By implementing the MaskingInterface interface, interaction pairs can be excluded duringNeighborListconstruction.The NeighborList class builds Verlet lists in parallel via a spatial decomposition.Hold the atom index and its symmetry operator.This class contains fields and methods for maintaining details of non-bonded cutoffs.A fixed schedule that balances pairwise work across threads.This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using aNeighborListfor anyCrystalspace group.The setFactors(i,k,lambdaMode) method is called every time through the inner PME loops, avoiding an "if (esv)" branch statement.The Reciprocal Space class computes the reciprocal space contribution toParticleMeshEwaldfor the AMOEBA force field.Restrain the position of atoms to their initial coordinates.The RowLoop class is used to parallelize placing onto a 3D gridThe RowRegion class is used to parallelize placing onto a 3D gridThe SliceLoop class is used to parallelize placing onto a 3D gridThe SliceLoop class is used to parallelize placing onto a 3D gridLoop over a list of atoms and assign their density to a grid.This class implements a spatial decomposition based on partitioning a grid into octants.The Van der Waals class computes Van der Waals interaction in parallel using aNeighborListfor anyCrystal.The trick: The setFactors(i,k) method is called every time through the inner VdW loop, avoiding an "if (esv)" branch statement.This class contains fields and methods for maintaining details of the van der Waals functional form.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. -
Classes in ffx.potential.nonbonded used by ffx.potential.nonbonded.implicitClassDescriptionThis Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a
NeighborList. -
Classes in ffx.potential.nonbonded used by ffx.potential.nonbonded.pmeClassDescriptionThis Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a
NeighborList.By implementing the MaskingInterface interface, interaction pairs can be excluded duringNeighborListconstruction.This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using aNeighborListfor anyCrystalspace group.The Reciprocal Space class computes the reciprocal space contribution toParticleMeshEwaldfor the AMOEBA force field. -
Classes in ffx.potential.nonbonded used by ffx.xrayClassDescriptionThe RowRegion class is used to parallelize placing onto a 3D gridThe SliceLoop class is used to parallelize placing onto a 3D gridThis class implements a spatial decomposition based on partitioning a grid into octants.