Package ffx.algorithms.mc

@ParametersAreNonnullByDefault package ffx.algorithms.mc

The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.

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.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.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
BoltzmannMC	The BoltzmannMC abstract class is a skeleton for Boltzmann-weighted Metropolis Monte Carlo simulations.
LambdaMove	Define an MC move to update lambda.
MCLoop	MCLoop class.
MCMove	The MCMove interface defines the basic functionality of a Monte Carlo move; that it can apply its move and revert it.
MDMove	Use MD as a coordinate based MC move.
MetropolisMC	The MetropolisMC interface defines the basic methods of a Metropolis Monte Carlo application.
MolecularMC	The MolecularMC class is a framework to take Monte Carlo steps on a molecular system.
MonteCarloListener	The MonteCarloListener will be notified at regular intervals during an MC algorithm.
RosenbluthCBMC	Conformational Biased Monte Carlo (applied to ALL torsions of a peptide side-chain).
RosenbluthChi0Move	Represents a random chi[0] spin of the target residue.
RosenbluthChiAllMove	Represents a Boltzmann-drawn spin of all residue torsions for use with RosenbluthCBMC (Configurational-Bias Monte Carlo).
RosenbluthChiAllMove.MODE	Mode of the RosenbluthChiAllMove instance.
RosenbluthOBMC	Orientational Biased Monte Carlo (as applied to chi0 torsion of peptide side-chains).