Package ffx.algorithms.dynamics

@ParametersAreNonnullByDefault package ffx.algorithms.dynamics

The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.

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.dynamics.integrators	The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats	The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
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.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
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
Barostat	The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.
MDEngine	Enumerates available molecular dynamics engines; presently limited to the FFX reference engine and the OpenMM engine.
MDVerbosity	Define the verbosity of the MolecularDynamics class.
MDWriteAction	Describe actions taken by writeFilesForStep.
MolecularDynamics	Run NVE, NVT, or NPT molecular dynamics.
MolecularDynamicsOpenMM	Runs Molecular Dynamics using OpenMM implementation
NonEquilbriumDynamics	NonEquilbriumDynamics is a class that contains methods to control non-equilibrium molecular dynamics simulations.
PhReplicaExchange	The PhReplicaExchange implements pH replica exchange.
ReplicaExchange	The ReplicaExchange implements temperature and lambda replica exchange methods.
WeightedEnsembleManager	This class implements the Weighted Ensemble algorithm.
WeightedEnsembleManager.OneDimMetric