Package ffx.algorithms.optimize

@ParametersAreNonnullByDefault package ffx.algorithms.optimize

The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.

Since:

1.0

Related Packages

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.optimize.anneal
ffx.algorithms.optimize.manybody
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.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.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).

Class	Description
ConformationScan	This class is for a configuration optimization of two small systems.
CrystalMinimize	Minimize the energy of a system to an RMS gradient per atom convergence criteria.
Minimize	Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
Minimize.MinimizationEngine	Enumerates available molecular minimization engines; presently limited to the FFX reference engine and the OpenMM engine.
MinimizeOpenMM	Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy.
PhMinimize	Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
RotamerOptimization	Optimize protein side-chain conformations and nucleic acid backbone conformations using rotamers.
RotamerOptimization.Algorithm	Rotamer Optimization Methods.
RotamerOptimization.Direction
RotamerOptimization.DistanceMethod	Allows get2BodyDistance to find the shortest distance between any two rotamers or two residues.
TitrationManyBody
TorsionSearch	TorsionSearch class for performing a torsion scan on a molecule in a molecular assembly.