Uses of Class
ffx.potential.MolecularAssembly

Packages that use MolecularAssembly
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 anneal package implements simulated annealing-based optimization, including an interface for annealing schedules and several concrete schedule implementations (linear, exponential, and flat-end) used to control temperature during optimization runs.
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 Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
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 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 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 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.
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 Real Space CLI package defines options for PicoCLI command line scripts.
The Parsers package reads and writes CCP4 map files.
The UI package provides views and controllers for manipulating molecular systems.
The Commands package implements a Client/Server interface between Force Field X and simulations.
The X-ray package implements support for X-ray and Neutron refinement.
The X-ray CLI package defines options for PicoCLI command line scripts.
The Parsers package reads CNS files and reads/writes MTZ files.