Uses of Class
ffx.potential.bonded.Atom

Packages that use Atom
Package
Description
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
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 Potential CLI package defines reusable options for PicoCLI command line scripts.
The constraint package implements holonomic constraint algorithms used during molecular dynamics and minimization, including CCMA, SETTLE, and SHAKE-style constraints (as well as charge constraints).
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 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 X-ray package implements support for X-ray and Neutron refinement.